https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/Recent changes to Strand InheritanceenFri, 05 Jul 2013 17:19:52 -0000https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v8 +++ v9 @@ -57,3 +57,14 @@ total | 5 | 5 | 5 | 4 pVal | 0.67 | 0.76 | 0.52 | 0.65 holm | 0.8 | 0.8 | 0.8 | 0.8 + + +**Jump to:** + +[Wiki Main Page](https://sourceforge.net/p/bait/wiki/Home/ "Wiki main page") +[What is Strand-seq and how does it work?](https://sourceforge.net/p/bait/wiki/Introduction%20to%20Strand-seq%20and%20BAIT/ "A brief outline of Strand-seq and the BAIT pipeline") +[Tutorial for strand inheritance studies](https://sourceforge.net/p/bait/wiki/Strand%20Inheritance/ "For immortal strand theory / silent sister hypothesis / epigenetic projects") +[Tutorial for sister chromatid exchange studies](https://sourceforge.net/p/bait/wiki/Sister%20Chromatid%20Exchange/ "For localization and counts of SCE, and comparison of SCE locations to genomic landscapes") +[Tutorial for identifying genomic rearrangements](https://sourceforge.net/p/bait/wiki/Identification%20of%20genomic%20rearrangements/ "For finding large genomic alterations including translocations, inversions and deletions") +[Tutorial for localization of orphan fragments](https://sourceforge.net/p/bait/wiki/Orphan%20Fragment%20Localization/ "For localizing unplaced and unlocalized scaffolds in chromosome/complete-stage genomes") +[Tutorial for building early stage genomes](https://sourceforge.net/p/bait/wiki/Genome%20Building/ "For clustering contigs from scaffold/chromosome-stage genomes into chromosomes and inferring relative orders") </pre> </div>Mark_HIllsFri, 05 Jul 2013 17:19:52 -0000https://sourceforge.netff892e10286859b9f7e41787ae16ac9969e8b203https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v7 +++ v8 @@ -13,6 +13,8 @@ Standard options to use in BAIT include: -r >This option identifies sister chromatid exchanges (for a detailed turorial, see [HERE](https://sourceforge.net/p/bait/wiki/Sister%20Chromatid%20Exchange/ "Tutorial for localization and counts of SCE, and comparison of SCE locations to genomic landscapes"). While SCEs are not essential in the identification of inherited strands, using this option allows BAIT to accurately determine which strands have been inherited for each chromosome. Any chromosome that has an SCE event is not counted as it has multiple strand inheritance patterns (the pattern will change after after an SCE event). With this option applied, BAIT will ignore chromosomes with SCE, and calculate the frequency of WW, WC and CC states for each remaining chromosomes across all libraries. Without this option selected, BAIT judges strand inheritance is based on a ratio between Watson and Crick reads for each chromosome; if the chromosome is >95% Crick it is called as CC, >95% Watson it is called as WW, 45-55% Watson it is called as WC, and any other ratio is called as potential SCE. This can cause issues if the library background is high, or if there is a SCE event that occupies less than 5% of the length of the chromosome. + + Output files ========== </pre> </div>Mark_HIllsWed, 03 Jul 2013 17:31:28 -0000https://sourceforge.net2903b247ab591c3ad0128009abe3614313feeca6https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v6 +++ v7 @@ -41,3 +41,17 @@ ------------------------- The Strand inheritance tables indicates a template inheritance state (WW, WC, CC, SCE or NA) for each library in a table format. Each row represents a library, and each column a chromosome. At the bottom of the table is totals for each state, the p-values, and the Holm corrected p-values. + +Library| chr1 | chr2 | chr3 | chr4 +-------|------|------|------|----- +Strand-seq1 | WC | WC | WW | CC +Strand-seq2 | WC | CC | WC | WC +Strand-seq3 | CC | CC | WW | WC +Strand-seq4 | WW | WC | CC | SCE +Strand-seq5 | WC | WC | WW | WC +total WW | 1 | 0 | 3 | 0 +total WC | 3 | 3 | 1 | 3 +total CC | 1 | 2 | 1 | 1 +total | 5 | 5 | 5 | 4 +pVal | 0.67 | 0.76 | 0.52 | 0.65 +holm | 0.8 | 0.8 | 0.8 | 0.8 </pre> </div>Mark_HIllsWed, 03 Jul 2013 00:13:51 -0000https://sourceforge.net56f72be85a30e65e880c3e13f0d29318c0cdbc6fhttps://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v5 +++ v6 @@ -29,11 +29,11 @@ This generates a series of files pertaining to several analysis streams. For strand inheritance the important pages are: -1. pie charts: Page 5 of the summary pdf that is generated. The pie charts present the frequency of WW, WC and CC inheritance patterns for each chromosome together with p values looking for significant deviations away from randomness. This provides a quick and easy visual assessment of each chromosome in a library context. Any calculated p-values also include a p-value after Holm correction to correctly adjust for multiple tests. The number of libraries included is given for each chromosome, as a particular chromosome is ignored from a library in which it has an SCE (eg, in 10 libraries if there are 2 libraries with SCEs in chr1 and 1 library with SCEs in chr2, 8 libraries will be used to calculate inheritance for chr1, and 9 libraries used to calculate inheritance in chr2). +>**pie charts**: Page 5 of the summary pdf that is generated. The pie charts present the frequency of WW, WC and CC inheritance patterns for each chromosome together with p values looking for significant deviations away from randomness. This provides a quick and easy visual assessment of each chromosome in a library context. Any calculated p-values also include a p-value after Holm correction to correctly adjust for multiple tests. The number of libraries included is given for each chromosome, as a particular chromosome is ignored from a library in which it has an SCE (eg, in 10 libraries if there are 2 libraries with SCEs in chr1 and 1 library with SCEs in chr2, 8 libraries will be used to calculate inheritance for chr1, and 9 libraries used to calculate inheritance in chr2).  -2. boxplots: Page 6 of the summary pdf. Boxplots overcome the problem of having to exclude chromosomes with SCE events. While pie charts only analyse chromosomes with a single strand inheritance state, the box plots show the states at a bin level, thus accepting chromosomes in which there has been a SCE. Each box represents a single chromosome, and the vertical axis represents the length of the chromosome. For each bin (set as default to 200kb, but can be changed using -w), the number of libraries where that bin is WW, WC or CC is calculated. For example, if chr1 had 100 bins and library1 was WW, each of the 100 bin states would be WW; if library2 had a SCE from WW to WC in bin 30, the first 30 bins would be WW, then the remaining 70 would be WC. This presents a profile of strand usage across the length of the chromosome. This can be very powerful, as if a particular chromosomal region is important for asymmetrical segregation, or if sorting is based on gene/protein expression that is expected to have different strand inheritance, the box plots will pick out the exact locations on the chromosome. +>**boxplots**: Page 6 of the summary pdf. Boxplots overcome the problem of having to exclude chromosomes with SCE events. While pie charts only analyse chromosomes with a single strand inheritance state, the box plots show the states at a bin level, thus accepting chromosomes in which there has been a SCE. Each box represents a single chromosome, and the vertical axis represents the length of the chromosome. For each bin (set as default to 200kb, but can be changed using -w), the number of libraries where that bin is WW, WC or CC is calculated. For example, if chr1 had 100 bins and library1 was WW, each of the 100 bin states would be WW; if library2 had a SCE from WW to WC in bin 30, the first 30 bins would be WW, then the remaining 70 would be WC. This presents a profile of strand usage across the length of the chromosome. This can be very powerful, as if a particular chromosomal region is important for asymmetrical segregation, or if sorting is based on gene/protein expression that is expected to have different strand inheritance, the box plots will pick out the exact locations on the chromosome.  </pre> </div>Mark_HIllsThu, 27 Jun 2013 22:15:05 -0000https://sourceforge.net61b2f9379642672a74fe7e287518e01cf23108c4https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v4 +++ v5 @@ -1,7 +1,7 @@ Introduction ========== -Strand inheritance has been proposed as a potential epigenetic system for asymmetric cell division. For example, a stem cell divides, where one daughter remains a stem cell, and the other daughter has differentiated into a less primitive cell type. It is possible this asymmetry is dictated by the relative distribution of protein or RNA when the cyoplasm is shared into the two daughter cells. It is also posible the location of the divided cells to an external niche directs this asymmetry. However, it has been proposed that the strands of DNA that are inherited may also play a role. Despite the fact that the two daughter cells will each inherit an identical copy of each chromosome, one cell will inherit a copy where the + strand acted as the template, and the other cell will inherit a copy where the - strand acted as a template. If newly-replicated DNA have some epigenetic differences to the unreplicated template strands, then this could drive asymmetry as genes expressed on the + strand will only be active in one cell and not the other. +Strand inheritance has been proposed as a potential epigenetic system for asymmetric cell division. For example, a stem cell divides, where one daughter remains a stem cell, and the other daughter has differentiated into a less primitive cell type. It is possible this asymmetry is dictated by the relative distribution of protein or RNA when the cytoplasm is shared into the two daughter cells. It is also possible the location of the divided cells to an external niche directs this asymmetry. However, it has been proposed that the strands of DNA that are inherited may also play a role. Despite the fact that the two daughter cells will each inherit an identical copy of each chromosome, one cell will inherit a copy where the + strand acted as the template, and the other cell will inherit a copy where the - strand acted as a template. If newly-replicated DNA have some epigenetic differences to the unreplicated template strands, then this could drive asymmetry as genes expressed on the + strand will only be active in one cell and not the other. Typical run @@ -12,7 +12,7 @@ Standard options to use in BAIT include: -r ->This option identifies sister chromatid exchanges (for a detailed turorial, see [HERE](https://sourceforge.net/p/bait/wiki/Sister%20Chromatid%20Exchange/ "Tutorial for localization and counts of SCE, and comparison of SCE locations to genomic landscapes"). While SCEs are not essential in the identification of inherited strands, using this option allows BAIT to accurately determine which strands have been inherited for each chromosome. Any chromosome that has an SCE event is not counted as it has multiple strand inheritance patterns (the pattern will change after after an SCE event). With this option applied, BAIT will ignore chromosomes with SCE, and calculate the frequency of WW, WC and CC states for each remaining chromosomes across all libraries. Without this option selected, BAIT judges strand inheritance is based on a ratio between Watson and Crick reads for each chromosome; if the chromosome is >95% Crick it is called as CC, >95% Watson it is called as WW, 45-55% Watson it is called as WC, and any other ratio is called as potential SCE. This can cause issues if the lirarby background is high, or if there is a SCE event that occupies less than 5% of the length of the chromosome. +>This option identifies sister chromatid exchanges (for a detailed turorial, see [HERE](https://sourceforge.net/p/bait/wiki/Sister%20Chromatid%20Exchange/ "Tutorial for localization and counts of SCE, and comparison of SCE locations to genomic landscapes"). While SCEs are not essential in the identification of inherited strands, using this option allows BAIT to accurately determine which strands have been inherited for each chromosome. Any chromosome that has an SCE event is not counted as it has multiple strand inheritance patterns (the pattern will change after after an SCE event). With this option applied, BAIT will ignore chromosomes with SCE, and calculate the frequency of WW, WC and CC states for each remaining chromosomes across all libraries. Without this option selected, BAIT judges strand inheritance is based on a ratio between Watson and Crick reads for each chromosome; if the chromosome is >95% Crick it is called as CC, >95% Watson it is called as WW, 45-55% Watson it is called as WC, and any other ratio is called as potential SCE. This can cause issues if the library background is high, or if there is a SCE event that occupies less than 5% of the length of the chromosome. Output files ========== @@ -20,7 +20,7 @@ The Standard Ideogram: ---------------------- -The standard BAIT ideogram has several key features. The reads are plotted as histograms on either side of ideograms representing the length of each chromosome. On the left, Watson reads are shown in orange, and on the right, Crick reads are shown in blue. The number of reads per Mb are displayed at the bottom of each histogram, to show the read density. If this density falls below 66% or above 133% of the average read density, chromosomes are called as monosomes or trisomes respectively. These are labelled under the chromosome together with the read percentage compared to average. On the top left of the ideogram plot is the sample name, and on the top right the number of SCE events and misorientations ('switches') identified. These numbers are blank if -r is not invoked. On the bottom right the read number and % coverage are shown (if the -c option is used) and on the bottom left, the overal reads per Mb is shown. +The standard BAIT ideogram has several key features. The reads are plotted as histograms on either side of ideograms representing the length of each chromosome. On the left, Watson reads are shown in orange, and on the right, Crick reads are shown in blue. The number of reads per Mb are displayed at the bottom of each histogram, to show the read density. If this density falls below 66% or above 133% of the average read density, chromosomes are called as monosomes or trisomes respectively. These are labelled under the chromosome together with the read percentage compared to average. On the top left of the ideogram plot is the sample name, and on the top right the number of SCE events and misorientations ('switches') identified. These numbers are blank if -r is not invoked. On the bottom right the read number and % coverage are shown (if the -c option is used) and on the bottom left, the overall reads per Mb is shown.  @@ -29,14 +29,15 @@ This generates a series of files pertaining to several analysis streams. For strand inheritance the important pages are: -1. pie charts: Page 5 of the summary pdf that is generated. The pie charts present the frequency of WW, WC and CC inheritance patterns for each chromosome together with p values looking for significant deviations away from randomness. This provides a quick and easy visual assement of each chromosome in a library context. Any calculated p-values also include a p-value after Holm correction to correctly adjust for multiple tests. The number of libraries included is given for each chromosome, as a particulat chromosome is ignored from a library in which it has an SCE (eg, in 10 libraries if there are 2 libraries with SCEs in chr1 and 1 library with SCEs in chr2, 8 libraries will be used to calculate inheritance for chr1, and 9 libraries used to calculate inheritance in chr2). +1. pie charts: Page 5 of the summary pdf that is generated. The pie charts present the frequency of WW, WC and CC inheritance patterns for each chromosome together with p values looking for significant deviations away from randomness. This provides a quick and easy visual assessment of each chromosome in a library context. Any calculated p-values also include a p-value after Holm correction to correctly adjust for multiple tests. The number of libraries included is given for each chromosome, as a particular chromosome is ignored from a library in which it has an SCE (eg, in 10 libraries if there are 2 libraries with SCEs in chr1 and 1 library with SCEs in chr2, 8 libraries will be used to calculate inheritance for chr1, and 9 libraries used to calculate inheritance in chr2). -![example pie chart plot](https://sourceforge.net/p/bait/screenshot/Screenshot-3.png "example pie chart plot" width=300) + -2. boxplots: Page 6 of the summary pdf. Boxplots overcome the problem of having to exclude chromosomes with SCE events. While pie charts only analyze chromosomes with a single strand inheritance state, the box plots show the states at a bin level, thus accepting chromosomes in which there has been a SCE. Each box represents a single chromosome, and the vertical axis represents the length of the chromosome. For each bin (set as default to 200kb, but can be changed using -w), the number of libraries where that bin is WW, WC or CC is calculated. For example, if chr1 had 100 bins and library1 was WW, each of the 100 bin states would be WW; if library2 had a SCE from WW to WC in bin 30, the first 30 bins would be WW, then the remaining 70 would be WC. This presents a profile of strand usage across the length of the chromosome. This can be very powerful, as if a particular chromosomal region is important for asymmetrical segregation, or if sorting is based on gene/protein expression that is expected to have different strand inheritance, the box plots will pick out the exact locations on the chromosome. +2. boxplots: Page 6 of the summary pdf. Boxplots overcome the problem of having to exclude chromosomes with SCE events. While pie charts only analyse chromosomes with a single strand inheritance state, the box plots show the states at a bin level, thus accepting chromosomes in which there has been a SCE. Each box represents a single chromosome, and the vertical axis represents the length of the chromosome. For each bin (set as default to 200kb, but can be changed using -w), the number of libraries where that bin is WW, WC or CC is calculated. For example, if chr1 had 100 bins and library1 was WW, each of the 100 bin states would be WW; if library2 had a SCE from WW to WC in bin 30, the first 30 bins would be WW, then the remaining 70 would be WC. This presents a profile of strand usage across the length of the chromosome. This can be very powerful, as if a particular chromosomal region is important for asymmetrical segregation, or if sorting is based on gene/protein expression that is expected to have different strand inheritance, the box plots will pick out the exact locations on the chromosome. - + Strand Inheritance Table: ------------------------- +The Strand inheritance tables indicates a template inheritance state (WW, WC, CC, SCE or NA) for each library in a table format. Each row represents a library, and each column a chromosome. At the bottom of the table is totals for each state, the p-values, and the Holm corrected p-values. </pre> </div>Mark_HIllsThu, 27 Jun 2013 22:03:43 -0000https://sourceforge.net10140304c18ae5d13d29890b072d4f2ee19d4bc7https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v3 +++ v4 @@ -22,7 +22,7 @@ The standard BAIT ideogram has several key features. The reads are plotted as histograms on either side of ideograms representing the length of each chromosome. On the left, Watson reads are shown in orange, and on the right, Crick reads are shown in blue. The number of reads per Mb are displayed at the bottom of each histogram, to show the read density. If this density falls below 66% or above 133% of the average read density, chromosomes are called as monosomes or trisomes respectively. These are labelled under the chromosome together with the read percentage compared to average. On the top left of the ideogram plot is the sample name, and on the top right the number of SCE events and misorientations ('switches') identified. These numbers are blank if -r is not invoked. On the bottom right the read number and % coverage are shown (if the -c option is used) and on the bottom left, the overal reads per Mb is shown. -[Standard BAIT ideogram](https://sourceforge.net/p/bait/screenshot/BAIT_output.jpg "Standard BAIT ideogram; including the -a option will print the same but with arrowheads over the SCE and switch regions") + The Standard Summary File: -------------------------- @@ -31,7 +31,7 @@ 1. pie charts: Page 5 of the summary pdf that is generated. The pie charts present the frequency of WW, WC and CC inheritance patterns for each chromosome together with p values looking for significant deviations away from randomness. This provides a quick and easy visual assement of each chromosome in a library context. Any calculated p-values also include a p-value after Holm correction to correctly adjust for multiple tests. The number of libraries included is given for each chromosome, as a particulat chromosome is ignored from a library in which it has an SCE (eg, in 10 libraries if there are 2 libraries with SCEs in chr1 and 1 library with SCEs in chr2, 8 libraries will be used to calculate inheritance for chr1, and 9 libraries used to calculate inheritance in chr2). - +![example pie chart plot](https://sourceforge.net/p/bait/screenshot/Screenshot-3.png "example pie chart plot" width=300) 2. boxplots: Page 6 of the summary pdf. Boxplots overcome the problem of having to exclude chromosomes with SCE events. While pie charts only analyze chromosomes with a single strand inheritance state, the box plots show the states at a bin level, thus accepting chromosomes in which there has been a SCE. Each box represents a single chromosome, and the vertical axis represents the length of the chromosome. For each bin (set as default to 200kb, but can be changed using -w), the number of libraries where that bin is WW, WC or CC is calculated. For example, if chr1 had 100 bins and library1 was WW, each of the 100 bin states would be WW; if library2 had a SCE from WW to WC in bin 30, the first 30 bins would be WW, then the remaining 70 would be WC. This presents a profile of strand usage across the length of the chromosome. This can be very powerful, as if a particular chromosomal region is important for asymmetrical segregation, or if sorting is based on gene/protein expression that is expected to have different strand inheritance, the box plots will pick out the exact locations on the chromosome. </pre> </div>Mark_HIllsThu, 27 Jun 2013 18:17:53 -0000https://sourceforge.net0d7af96baf4ac6a15dae839b93150e84a9164a67https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -12,17 +12,31 @@ Standard options to use in BAIT include: -r -This option identifies sister chromatid exchanges (for a detailed turorial, see [HERE](https://sourceforge.net/p/bait/wiki/Sister%20Chromatid%20Exchange/ "Tutorial for localization and counts of SCE, and comparison of SCE locations to genomic landscapes"). While SCEs are not essential in the identification of inherited strands, using this option allows BAIT to accurately determine which strands have been inherited for each chromosome. Any chromosome that has an SCE event is not counted as it has multiple strand inheritance patterns (the pattern will change after after an SCE event). With this option applied, BAIT will ignore chromosomes with SCE, and calculate the frequency of WW, WC and CC states for each remaining chromosomes across all libraries. Without this option selected, BAIT judges strand inheritance is based on a ratio between Watson and Crick reads for each chromosome; if the chromosome is >95% Crick it is called as CC, >95% Watson it is called as WW, 45-55% Watson it is called as WC, and any other ratio is called as potential SCE. This can cause issues if the lirarby background is high, or if there is a SCE event that occupies less than 5% of the length of the chromosome. +>This option identifies sister chromatid exchanges (for a detailed turorial, see [HERE](https://sourceforge.net/p/bait/wiki/Sister%20Chromatid%20Exchange/ "Tutorial for localization and counts of SCE, and comparison of SCE locations to genomic landscapes"). While SCEs are not essential in the identification of inherited strands, using this option allows BAIT to accurately determine which strands have been inherited for each chromosome. Any chromosome that has an SCE event is not counted as it has multiple strand inheritance patterns (the pattern will change after after an SCE event). With this option applied, BAIT will ignore chromosomes with SCE, and calculate the frequency of WW, WC and CC states for each remaining chromosomes across all libraries. Without this option selected, BAIT judges strand inheritance is based on a ratio between Watson and Crick reads for each chromosome; if the chromosome is >95% Crick it is called as CC, >95% Watson it is called as WW, 45-55% Watson it is called as WC, and any other ratio is called as potential SCE. This can cause issues if the lirarby background is high, or if there is a SCE event that occupies less than 5% of the length of the chromosome. Output files ========== The Standard Ideogram: +---------------------- -The standard BAIT ideogram has several key features. The reads are plotted as hostograms on either side of ideograms representing the length of each chromosome. On the left, Watson reads are shown in orange, and on the right, Crick reads are shown in blue. The number of reads per Mb are displayed at the bottom of each histogram, to show the read density. If this density falls below 66% or above 133% of the average read density, chromosomes are called as monosomes or trisomes respectively. These are labelled under the chromosome together with the read percentage compared to average. On the top left of the ideogram plot is the sample name, and on the top right the number of SCE events and misorientations ('switches') identified. These numbers are blank if -r is not invoked. On the bottom right the read number and % coverage are shown (if the -c option is used) and on the bottom left, the overal reads per Mb is shown. +The standard BAIT ideogram has several key features. The reads are plotted as histograms on either side of ideograms representing the length of each chromosome. On the left, Watson reads are shown in orange, and on the right, Crick reads are shown in blue. The number of reads per Mb are displayed at the bottom of each histogram, to show the read density. If this density falls below 66% or above 133% of the average read density, chromosomes are called as monosomes or trisomes respectively. These are labelled under the chromosome together with the read percentage compared to average. On the top left of the ideogram plot is the sample name, and on the top right the number of SCE events and misorientations ('switches') identified. These numbers are blank if -r is not invoked. On the bottom right the read number and % coverage are shown (if the -c option is used) and on the bottom left, the overal reads per Mb is shown. + +[Standard BAIT ideogram](https://sourceforge.net/p/bait/screenshot/BAIT_output.jpg "Standard BAIT ideogram; including the -a option will print the same but with arrowheads over the SCE and switch regions") The Standard Summary File: +-------------------------- -This generates a series of pie charts on the summary pdf that is generated, together with p values looking for significant diviations away from randomness. +This generates a series of files pertaining to several analysis streams. For strand inheritance the important pages are: + +1. pie charts: Page 5 of the summary pdf that is generated. The pie charts present the frequency of WW, WC and CC inheritance patterns for each chromosome together with p values looking for significant deviations away from randomness. This provides a quick and easy visual assement of each chromosome in a library context. Any calculated p-values also include a p-value after Holm correction to correctly adjust for multiple tests. The number of libraries included is given for each chromosome, as a particulat chromosome is ignored from a library in which it has an SCE (eg, in 10 libraries if there are 2 libraries with SCEs in chr1 and 1 library with SCEs in chr2, 8 libraries will be used to calculate inheritance for chr1, and 9 libraries used to calculate inheritance in chr2). + + + +2. boxplots: Page 6 of the summary pdf. Boxplots overcome the problem of having to exclude chromosomes with SCE events. While pie charts only analyze chromosomes with a single strand inheritance state, the box plots show the states at a bin level, thus accepting chromosomes in which there has been a SCE. Each box represents a single chromosome, and the vertical axis represents the length of the chromosome. For each bin (set as default to 200kb, but can be changed using -w), the number of libraries where that bin is WW, WC or CC is calculated. For example, if chr1 had 100 bins and library1 was WW, each of the 100 bin states would be WW; if library2 had a SCE from WW to WC in bin 30, the first 30 bins would be WW, then the remaining 70 would be WC. This presents a profile of strand usage across the length of the chromosome. This can be very powerful, as if a particular chromosomal region is important for asymmetrical segregation, or if sorting is based on gene/protein expression that is expected to have different strand inheritance, the box plots will pick out the exact locations on the chromosome. + + Strand Inheritance Table: +------------------------- + </pre> </div>Mark_HIllsThu, 27 Jun 2013 18:00:36 -0000https://sourceforge.net782a5b33ca02ce12318d0d4f62dcf58bfabe5421https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -0,0 +1,28 @@ +Introduction +========== + +Strand inheritance has been proposed as a potential epigenetic system for asymmetric cell division. For example, a stem cell divides, where one daughter remains a stem cell, and the other daughter has differentiated into a less primitive cell type. It is possible this asymmetry is dictated by the relative distribution of protein or RNA when the cyoplasm is shared into the two daughter cells. It is also posible the location of the divided cells to an external niche directs this asymmetry. However, it has been proposed that the strands of DNA that are inherited may also play a role. Despite the fact that the two daughter cells will each inherit an identical copy of each chromosome, one cell will inherit a copy where the + strand acted as the template, and the other cell will inherit a copy where the - strand acted as a template. If newly-replicated DNA have some epigenetic differences to the unreplicated template strands, then this could drive asymmetry as genes expressed on the + strand will only be active in one cell and not the other. + + +Typical run +========== + + BAIT -rav -o TypicalRun + + +Standard options to use in BAIT include: +-r +This option identifies sister chromatid exchanges (for a detailed turorial, see [HERE](https://sourceforge.net/p/bait/wiki/Sister%20Chromatid%20Exchange/ "Tutorial for localization and counts of SCE, and comparison of SCE locations to genomic landscapes"). While SCEs are not essential in the identification of inherited strands, using this option allows BAIT to accurately determine which strands have been inherited for each chromosome. Any chromosome that has an SCE event is not counted as it has multiple strand inheritance patterns (the pattern will change after after an SCE event). With this option applied, BAIT will ignore chromosomes with SCE, and calculate the frequency of WW, WC and CC states for each remaining chromosomes across all libraries. Without this option selected, BAIT judges strand inheritance is based on a ratio between Watson and Crick reads for each chromosome; if the chromosome is >95% Crick it is called as CC, >95% Watson it is called as WW, 45-55% Watson it is called as WC, and any other ratio is called as potential SCE. This can cause issues if the lirarby background is high, or if there is a SCE event that occupies less than 5% of the length of the chromosome. + +Output files +========== + +The Standard Ideogram: + +The standard BAIT ideogram has several key features. The reads are plotted as hostograms on either side of ideograms representing the length of each chromosome. On the left, Watson reads are shown in orange, and on the right, Crick reads are shown in blue. The number of reads per Mb are displayed at the bottom of each histogram, to show the read density. If this density falls below 66% or above 133% of the average read density, chromosomes are called as monosomes or trisomes respectively. These are labelled under the chromosome together with the read percentage compared to average. On the top left of the ideogram plot is the sample name, and on the top right the number of SCE events and misorientations ('switches') identified. These numbers are blank if -r is not invoked. On the bottom right the read number and % coverage are shown (if the -c option is used) and on the bottom left, the overal reads per Mb is shown. + +The Standard Summary File: + +This generates a series of pie charts on the summary pdf that is generated, together with p values looking for significant diviations away from randomness. + +Strand Inheritance Table: </pre> </div>Mark_HIllsWed, 26 Jun 2013 23:59:34 -0000https://sourceforge.net3fd9f062932b3d074b770cadaed786f1856fa851https://sourceforge.net/p/bait/wiki/Strand%2520Inheritance/Mark_HIllsTue, 25 Jun 2013 17:41:57 -0000https://sourceforge.netd995085323b17d58a2e2d0d12b7d820c66a5f708