Recent changes to validation_fix_seg

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 13:14:42 -0000

--- v7
+++ v8
@@ -67,3 +67,4 @@
 [[img src=fixseg.mhp.png width=900]]

 ## Conclusion
+The population frequency of all insertions, ie. segregating and fixed insertions of all 123 TE families is correctly estimated. Also the order of the insertion was correctly inferred

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 13:13:25 -0000

--- v6
+++ v7
@@ -38,7 +38,7 @@
 ~~~~~
 python ~/dev/manna/cluster-msa.py --clusters "" --sample-IDs "" --quick-rm fixseg.fasta.out > fixseq.manna
 ~~~~~
-An example from the Manna alignment with segregating insertions
+An example from the Manna alignment with segregating insertions.
 ~~~~~~
 ...
 -       -       -       INVADER6        4885.0  0.0     -       -       -       INVADER6        4885.0  0.0     -       -       -
@@ -53,7 +53,7 @@

 ...
 ~~~~~~
-In this example the INVADER6 is segregating and only occurin in two samples/strains, whereas HELITRON1_DM is fixed.
+In this example the INVADER6 is segregating and only occurin in two samples/strains, whereas HELITRON1_DM is fixed.  Note that this is the intermediate output, more details (eg. the strand of the TE insertions and the position in the query can be obtained via --output-detail


 ## Expected vs observed and Manhatten plot

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 13:11:43 -0000

--- v5
+++ v6
@@ -38,6 +38,23 @@
 ~~~~~
 python ~/dev/manna/cluster-msa.py --clusters "" --sample-IDs "" --quick-rm fixseg.fasta.out > fixseq.manna
 ~~~~~
+An example from the Manna alignment with segregating insertions
+~~~~~~
+...
+-       -       -       INVADER6        4885.0  0.0     -       -       -       INVADER6        4885.0  0.0     -       -       -
+HELITRON1_DM    564.0   0.0     HELITRON1_DM    564.0   0.0     HELITRON1_DM    564.0   0.0     HELITRON1_DM    564.0   0.0     HELITRON1_DM    564.0   0.0
+-       -       -       -       -       -       -       -       -       INVADER3        5484.0  0.0     -       -       -
+BS4     754.0   0.0     BS4     754.0   0.0     BS4     754.0   0.0     BS4     754.0   0.0     BS4     754.0   0.0
+RT1C    5443.0  0.0     RT1C    5443.0  0.0     -       -       -       -       -       -       RT1C    5443.0  0.0
+TABOR   7345.0  0.0     TABOR   7345.0  0.0     TABOR   7345.0  0.0     TABOR   7345.0  0.0     TABOR   7345.0  0.0
+-       -       -       DMRER1DM        5356.0  0.0     DMRER1DM        5356.0  0.0     -       -       -       -       -       -
+DME278684       5108.0  0.0     DME278684       5108.0  0.0     DME278684       5108.0  0.0     DME278684       5108.0  0.0     DME278684       5108.0  0.0
+DM_ROO  9092.0  0.0     DM_ROO  9092.0  0.0     DM_ROO  9092.0  0.0     -       -       -       -       -       -
+
+...
+~~~~~~
+In this example the INVADER6 is segregating and only occurin in two samples/strains, whereas HELITRON1_DM is fixed.
+

 ## Expected vs observed and Manhatten plot

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 13:09:16 -0000

--- v4
+++ v5
@@ -33,9 +33,18 @@
 ~~~~~~
 RepeatMasker --frag 2000000 -pa 1 -no_is -s -nolow -dir . -lib ../teseq-clean-ml100noS4.fasta fixseg.fasta  
 ~~~~~~
+## Manna alignment

+~~~~~
+python ~/dev/manna/cluster-msa.py --clusters "" --sample-IDs "" --quick-rm fixseg.fasta.out > fixseq.manna
+~~~~~

+## Expected vs observed and Manhatten plot

+~~~~~~
+python ~/dev/manna/validation/manna-vs-pgd-mhp.py --min-len 100 --max-div 5 --manna fixseq.manna --pgd fixseg.pgd > fixseq.mhp 
+R --vanilla --args fixseg.mhp < ~/dev/manna/validation/manhatten.R
+~~~~~~

 # Results
 [[img src=fixseg.mhp.png width=900]]

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 13:06:02 -0000

--- v3
+++ v4
@@ -1,10 +1,40 @@
 [TOC]

 # Introduction
-Here we simulate a scenario with alternating fixed and segregating insertions for each TE family. 
-In this validation we will be brief and mostly only show the commands. For a more comprehensive explanation of our validation approach **please read** [validation_fixed] first.
+Here we simulate a scenario with alternating fixed and segregating insertions for each TE family. For each of the 123 TE families we simulate one fixed (count of 5) and one segregating (count between 1 and 4) TE insertion. Fixed and segregating insertions are alternating.
+In this validation we will be brief and mostly solely show the commands. For a more comprehensive explanation of our validation approach **please read** [validation_fixed] first.
 #  Material and Methods
-All files are available at 
+##Data
+All files of this validation are available at <https: files="" manna="" sourceforge.net="" val2-fixseg="" validation="" projects="">
+
+## pgd
+We use a pgd file that specifies alternating fixed and segregating TE insertions (fixseg.pgd see availablilty above)
+An example from the file:
+
+~~~~~~
+...
+46491 52 52 52 52 52
+47653 73 * 73 73 73
+48844 42 42 42 42 42
+50089 * 12 12 12 *
+51455 122 122 122 122 122
+52164 * * 75 * *
+...
+~~~~~~
+**Note**: A star indicates that a TE (the integer number is the ID of a TE) is missing in a given sample/strain. For example an insertion of the TE '75' is segregating and only occuring in a single individual whereas the insertion of the TE 122 is fixed, occuring in all indivdiuals. For more details see documentation of SimulaTE.
+
+## popopulation genome
+
+~~~~~~
+python ~/dev/simulates/build-population-genome.py --chassis ../chasis.txt --pgd fixseg.pgd --te-seqs ../teseq.fasta --output fixseg.fasta     
+~~~~~~
+## RepeatMasking
+
+~~~~~~
+RepeatMasker --frag 2000000 -pa 1 -no_is -s -nolow -dir . -lib ../teseq-clean-ml100noS4.fasta fixseg.fasta  
+~~~~~~
+
+


 # Results
</https:>

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 12:56:30 -0000

--- v2
+++ v3
@@ -2,5 +2,12 @@

 # Introduction
 Here we simulate a scenario with alternating fixed and segregating insertions for each TE family. 
-In this validation I will be brief and mostly only show the commands. In order to understand our validation approach please read [validation_fixed] first.
-# Validation
+In this validation we will be brief and mostly only show the commands. For a more comprehensive explanation of our validation approach **please read** [validation_fixed] first.
+#  Material and Methods
+All files are available at 
+
+
+# Results
+[[img src=fixseg.mhp.png width=900]]
+
+## Conclusion

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 12:53:46 -0000

validation_fix_seg modified by Robert Kofler

Robert Kofler — Tue, 19 Jan 2021 10:17:42 -0000

Introduction
Validation

Introduction

Here we simulate a scenario with alternating fixed and segregating insertions for each TE family.
In this validation I will be brief and mostly only show the commands. In order to understand our validation approach please read [validation_fixed] first.