Output_Files modified by NOBEL89

NOBEL89 — Sat, 27 Jul 2013 13:58:33 -0000

--- v2
+++ v3
@@ -61,8 +61,8 @@
             is useful for users to select the interesting fusion events.
             Set config parameter 'PA_s09_draw_fusion_expression_svg' as 'yes', and enjoy this figure.
             click here for more information about SOAPfuse fusion figure.
-       click here to see one instance of TMPRSS2-ERG from one prostate cancer sample.
-       click here to see one instance of somatic KIF5B-RET from one lung cancer patient.
+       click here to see one instance of TMPRSS2-ERG from one prostate cancer sample.
+       click here to see one instance of somatic KIF5B-RET from one lung cancer patient.
             Note:
             'SOAPfuse fusion figure' is totally designed and achieved by Wenlong Jia in BGI. We will
             apply for a patent for this figure.
@@ -74,8 +74,8 @@
             fused-at-exon-edge-or-not and whether-is-somatic (in somatic running mode). It is also useful
             for users to select the interesting fusion events.
             click here for more information about SOAPfuse 3D landscape figure of fusion.
-            click here to see one instance of one prostate cancer sample harboring TMPRSS2-ERG.
-            click here to see one instance of one lung cancer patient harboring somatic KIF5B-RET.
+            click here to see one instance of one prostate cancer sample harboring TMPRSS2-ERG.
+            click here to see one instance of one lung cancer patient harboring somatic KIF5B-RET.
             Note:
             'SOAPfuse 3D landscape figure of fusion' is also totally designed and achieved by Wenlong Jia
             in BGI. Using 3D scale to display bioinformatic value distribution is common, but to our knowledge,

Output_Files modified by NOBEL89

NOBEL89 — Sat, 27 Jul 2013 04:25:28 -0000

--- v1
+++ v2
@@ -1,4 +1,4 @@
-[Output Files]()
+Output Files
 =
 All final results are stored in this directory:

   $ cd /out_directory/final_fusion_genes/sample-ID_or_patient-ID/

Output_Files modified by NOBEL89

NOBEL89 — Sat, 27 Jul 2013 04:25:01 -0000

ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround a code snippet with "~~~~"?

<b style="color:green">[Output Files]()</b>
=
<b>All final results</b> are stored in this directory:
<pre class="code" style="color:blue">   <b>$</b> cd /<b style="color:red">out_directory</b>/final_fusion_genes/<b style="color:orange">sample-ID_or_patient-ID</b>/</pre>
 <b style="color:red">Note:</b> the following description is for <u><b style="color: red" title="v1.24 has some results below, but directory layout is different.">v1.25</b></u>, click <a href="https://sourceforge.net/p/soapfuse/wiki/old.final.format.v1.22.for.SOAPfuse" title="check the format of old version v1.22">here</a> to see old format of <b>v1.22</b>.

1.    <h4 style="border-bottom: 1px dotted silver;"><b style="color:orange">sample-ID_or_patient-ID</b>.final.Fusion.specific.for.genes</h4>
    This text file contains the predicted fusion events specific for genes. The <u>format</u> of this file is:
    <pre class="code" style="color:blue"><b>Column_NO.</b>     <b>Descriptions</b><br/>   1           up stream fusion gene (5' partner)<br/>   2           chromosome of up stream fusion partner<br/>   3           strand of up stream fusion partner<br/>   4           genome junction position of up stream fusion partner<br/>   5           <a href="https://sourceforge.net/p/soapfuse/wiki/location-of-junction-point.for.SOAPfuse" title="check location of junction point"><em>location</em></a> of up stream fusion partner's junction point<br/>   6           down stream fusion gene (3' partner)<br/>   7           chromosome of down stream fusion partner<br/>   8           strand of down stream fusion partner<br/>   9           genome junction position of down stream fusion partner<br/>  10           location of down stream fusion partner's junction point<br/>  11           <i style="color: red"><u title="formats as 'tumor/control' in somatic mode, like '65/2', means there are 65 span-reads from tumor sample, and 2 span-reads from control sample">number</u></i> of span-reads (details in <b>sample-ID</b>.final.Span_reads)<br/>  12           <i style="color: red"><u title="formats as 'tumor/control' in somatic mode">number</u></i> of junc-reads (details in <b>sample-ID</b>.final.Junc_reads)<br/>  13           <a href="https://sourceforge.net/p/soapfuse/wiki/classification-of-fusions.for.SOAPfuse" title="check classification of fusion"><em>classification</em></a> of fusions<br/>  14           <a href="https://sourceforge.net/p/soapfuse/wiki/downstream-frameshift-definition.for.SOAPfuse" title="check the frameshift definition">whether down stream fusion partner is frame-shift or in-frame-shift</a><br/></pre>

+     <h4 style="border-bottom: 1px dotted silver;"><b style="color:orange">sample-ID_or_patient-ID</b>.final.Fusion.specific.for.trans</h4>
    As we know, each gene has its specific transcript isoform(s), and lots of genes have multiple isoforms. From v1.24 version, SOAPfuse detects fusion transcripts for each transcript isoform. For example, one fusion partner, <b>Gene-A</b>, its junction point may be covered by several transcript isoforms, such as <b>A-001</b> and <b>A-201</b>. And its fusion partner, <b>Gene-B</b>, is also in the same situation. So, for one fusion gene pair (<b>A-B</b>), you could find several corresponding fusion transcripts, each one consists of one isoform of <b>Gene-A</b> and one isoform of <b>Gene-B</b>.
    This text file contains the predicted fusion events specific for transcript isoforms. The <u>format</u> of this file is:
    <pre class="code" style="color:blue"><b>Column_NO.</b>     <b>Descriptions</b><br/>   1           up stream gene (5' partner)<br/>   2           up stream transcript isoform<br/>   3           chromosome of up stream fusion partner<br/>   4           strand of up stream fusion partner<br/>   5           transcript junction position of up stream fusion partner<br/>   6           genome junction position of up stream fusion partner<br/>   7           <a href="https://sourceforge.net/p/soapfuse/wiki/location-of-junction-point.for.SOAPfuse" title="check location of junction point"><em>location</em></a> of up stream fusion partner's junction point<br/>   8           down stream gene (3' partner)<br/>   9           down stream transcript isoform<br/>  10           chromosome of down stream fusion partner<br/>  11           strand of down stream fusion partner<br/>  12           transcript junction position of down stream fusion partner<br/>  13           genome junction position of down stream fusion partner<br/>  14           location of down stream fusion partner's junction point<br/>  15           <i style="color: red"><u title="formats as 'tumor/control' in somatic mode, like '65/2', means there are 65 span-reads from tumor sample, and 2 span-reads from control sample">number</u></i> of span-reads (details in <b>sample-ID</b>.final.Span_reads)<br/>  16           <i style="color: red"><u title="formats as 'tumor/control' in somatic mode">number</u></i> of junc-reads (details in <b>sample-ID</b>.final.Junc_reads)<br/>  17           <a href="https://sourceforge.net/p/soapfuse/wiki/classification-of-fusions.for.SOAPfuse" title="check classification of fusion"><em>classification</em></a> of fusions<br/>  18           <a href="https://sourceforge.net/p/soapfuse/wiki/downstream-frameshift-definition.for.SOAPfuse" title="check the frameshift definition">whether down fusion partner is frame-shift or in-frame-shift</a><br/>  19           <i style="color: red"><u title="type of each isoform is noted in the column NO.2 of Ensembl GTF file, just check it">type</u></i> of up stream fusion isoforms<br/>  20           type of down stream fusion isoforms<br/>  21           the <i style="color: red"><u title="utr3/utr5/coding_region/intron(nearest_area)">area</u></i> where up stream juction point locates<br/>  22           the area where down stream juction point locates<br/>  23           whether the up stream isoform has the start codon (in <i style="color: red"><u title="just check the Ensembl database, not concern with fusion structure">database</u></i>)<br/>  24           whether the up stream isoform has the stop codon (in database)<br/>  25           whether the down stream isoform has the start codon (in database)<br/>  26           whether the down stream isoform has the stop codon (in database)<br/>  27           whether the fusion structure has the stop codon<br/>  28           <a href="https://sourceforge.net/p/soapfuse/wiki/downstream-frameshift-definition.for.SOAPfuse" title="check the information of fusion peptide chain">the information of fusion peptide chain</a><br/></pre>

+     <h4 style="border-bottom: 1px dotted silver;"><b style="color:orange">sample-ID_or_patient-ID</b>.final.Span_reads</h4>
    This text file contains the detailed information of <b>span-reads</b>.
    <br/> 

+     <h4 style="border-bottom: 1px dotted silver;"><b style="color:orange">sample-ID_or_patient-ID</b>.final.Junc_reads</h4>
    This text file contains the detailed information of <b>junc-reads</b>.
    <br/> 

+     <h4 style="border-bottom: 1px dotted silver;">initial_fusions/</h4>
    This directory contains the initial fusion events before filtering.
    <br/> 

+     <h4 style="border-bottom: 1px dotted silver;">abandon_fusions/</h4>
    This directory contains the fusion events <b>abandoned</b> by different filterings.
    <br/> 

+     <h4 style="border-bottom: 1px dotted silver;">analysis/</h4>
    This directory contains the <b style="color:red">further analysis</b> of final fusion events.

    *  <b>In </b><b style="color: red">For_RT-PCR_validation</b><b> directory</b>
        <b style="color:green">a.</b> <b style="color:orange">sample-ID_or_patient-ID</b><b>.trans.fused.seq.for.RT-PCR</b>
        &nbsp;&nbsp;&nbsp;&nbsp;This text file contains the bilateral segment around junction point of each fusion transcript. It
        &nbsp;&nbsp;&nbsp;&nbsp;is corresponding to the <i><b style="color:orange">sample-ID_or_patient-ID</b>.final.Fusion.specific.for.trans</i> file. The up
        &nbsp;&nbsp;&nbsp;&nbsp;stream segment is separated with the down stream segment with vertical line '|'. The segments are
        &nbsp;&nbsp;&nbsp;&nbsp;very useful for users to construct the primers for their further RT-PCR validation experiments
        &nbsp;&nbsp;&nbsp;&nbsp;of concerned fusion events. It has been proved useful and correct by several fusion research
        &nbsp;&nbsp;&nbsp;&nbsp;projects in BGI.<br/>
        &nbsp;&nbsp;&nbsp;&nbsp;<u><b style="color:blue">Format</b></u>:
        <pre class="code" style="color:blue">    <b>Column_NO.</b>     <b>Descriptions</b><br/>       1           fusion event specific for genes<br/>       2           fusion event specific for transcript isoforms<br/>       3           bilateral fusion segments separated by '|'<br/></pre>

    *  <b>In </b><b style="color: red">For_peptides_analysis</b><b> directory</b>
        <b style="color:green">a.</b> <b style="color:orange">sample-ID_or_patient-ID</b><b>.trans.fusion.peptide.chain</b>
        &nbsp;&nbsp;&nbsp;&nbsp;This text file contains the predicted fusion peptide chains corresponding to all fusion
        &nbsp;&nbsp;&nbsp;&nbsp;transcripts that are annotated as 'inframe-shift' in <i><b>sample-ID_or_patient-ID</b>.final.
        &nbsp;&nbsp;&nbsp;&nbsp;Fusion.specific.for.trans</i> file. You can use the peptide chain string to study the domain
        &nbsp;&nbsp;&nbsp;&nbsp;regions in <a href="http://www.ebi.ac.uk/Tools/pfa/iprscan/" title="go to iprscan">iprscan</a> website.<br/>
        &nbsp;&nbsp;&nbsp;&nbsp;<u><b style="color:blue">Format</b></u>:
        <pre class="code" style="color:blue">   <b>Column_NO.</b>     <b>Descriptions</b><br/>       1           fusion event specific for transcript isoforms<br/>       2           <i style="color: red"><u title="upper cases are the translated part">whole fusion segment</u></i><br/>       3           <i style="color: red"><u title="coresponding to the upper cases in column NO.2">fusion peptide chain string</u></i><br/></pre>

    *  <b>In </b><b style="color: red">figures</b><b> directory</b>

        <b style="color:green">a.</b> <b style="color:orange">fusions_expression</b> <b>sub-directory</b>
        &nbsp;&nbsp;&nbsp;&nbsp;This sub-directory contains the so-called '<b style="color: red">SOAPfuse fusion figure</b>' (<i>svg/png</i>) of each fusion
        &nbsp;&nbsp;&nbsp;&nbsp;events. This figure merges the old fusion figure and gene expression figure (in <i>v1.22</i>), clearly
        &nbsp;&nbsp;&nbsp;&nbsp;showing the transcript junction point, genome junction point and supporting reads alignment. It
        &nbsp;&nbsp;&nbsp;&nbsp;is useful for users to select the interesting fusion events.
        &nbsp;&nbsp;&nbsp;&nbsp;Set config parameter '<b>PA_s09_draw_fusion_expression_svg</b>' as '<b>yes</b>', and enjoy this figure.
        &nbsp;&nbsp;&nbsp;&nbsp;click <a href="https://sourceforge.net/p/soapfuse/wiki/SOAPfuse.fusions.figure.note.for.SOAPfuse" title="check more info about SOAPfuse fusion figure">here</a> for more information about <b style="color: red">SOAPfuse fusion figure</b>.
	&nbsp;&nbsp;&nbsp;&nbsp;click <a href="https://sourceforge.net/p/soapfuse/wiki/Home/attachment/SOAPfuse.fusions.figure.TMPRSS2-ERG.prostate.cancer.for.SOAPfuse.png" title="check instance of sample analyzed in single-sample mode, pls understand other info is replaced by 'XXX'. As the figure amount is large, pls wait to load">here</a> to see one instance of <i style="color: red">TMPRSS2-ERG</i> from one prostate cancer sample.
	&nbsp;&nbsp;&nbsp;&nbsp;click <a href="https://sourceforge.net/p/soapfuse/wiki/Home/attachment/SOAPfuse.fusions.figure.KIF5B-RET.lung.cancer.for.SOAPfuse.png" title="check instance of sample analyzed in somatic mode, pls understand other info is replaced by 'XXX'. As the figure amount is large, pls wait to load">here</a> to see one instance of somatic <i style="color: red">KIF5B-RET</i> from one lung cancer patient.
        &nbsp;&nbsp;&nbsp;&nbsp;<b style="color:red">Note:</b>
        &nbsp;&nbsp;&nbsp;&nbsp;'<b style="color:red">SOAPfuse fusion figure</b>' is totally designed and achieved by Wenlong Jia in BGI. We will
        &nbsp;&nbsp;&nbsp;&nbsp;apply for a patent for this figure.

        <b style="color:green">b.</b> <b style="color:orange">landscape_of_fusions</b> <b>sub-directory</b>
        &nbsp;&nbsp;&nbsp;&nbsp;This sub-directory contains the so-called '<b style="color: red">SOAPfuse 3D landscape figure of fusion</b>' (<i>svg/png</i>)
        &nbsp;&nbsp;&nbsp;&nbsp;of concerned sample/patient. This figure displays all detected fusion events in 3D pillar array.
        &nbsp;&nbsp;&nbsp;&nbsp;Fusion events are shown with SOAPfuse-score, Fusion-type, inframe-shift-or-not,
        &nbsp;&nbsp;&nbsp;&nbsp;fused-at-exon-edge-or-not and whether-is-somatic (in somatic running mode). It is also useful
        &nbsp;&nbsp;&nbsp;&nbsp;for users to select the interesting fusion events.
        &nbsp;&nbsp;&nbsp;&nbsp;click <a href="https://sourceforge.net/p/soapfuse/wiki/fusions.landscape.3D.note.for.SOAPfuse" title="check more info about SOAPfuse 3D landscape figure of fusion">here</a> for more information about <b style="color: red">SOAPfuse 3D landscape figure of fusion</b>.
        &nbsp;&nbsp;&nbsp;&nbsp;click <a href="https://sourceforge.net/p/soapfuse/wiki/Home/attachment/fusions.landscape.3D.TMPRSS2-ERG.prostate.cancer.for.SOAPfuse.png" title="check instance of sample analyzed in single-sample mode, pls understand other info is replaced by 'XXX'.">here</a> to see one instance of one prostate cancer sample harboring <i style="color: red">TMPRSS2-ERG</i>.
        &nbsp;&nbsp;&nbsp;&nbsp;click <a href="https://sourceforge.net/p/soapfuse/wiki/Home/attachment/fusions.landscape.3D.KIF5B-RET.lung.cancer.for.SOAPfuse.png" title="check instance of sample analyzed in somatic mode, pls understand other info is replaced by 'XXX'.">here</a> to see one instance of one lung cancer patient harboring somatic <i style="color: red">KIF5B-RET</i>.
        &nbsp;&nbsp;&nbsp;&nbsp;<b style="color: red">Note:</b>
        &nbsp;&nbsp;&nbsp;&nbsp;'<b style="color:red">SOAPfuse 3D landscape figure of fusion</b>' is also totally designed and achieved by Wenlong Jia
        &nbsp;&nbsp;&nbsp;&nbsp;in BGI. Using 3D scale to display bioinformatic value distribution is common, but to our knowledge,
        &nbsp;&nbsp;&nbsp;&nbsp;this is the first time that it is used in the fusion gene research.<br/>
        <br/>

Recent changes to Output_Files

Output_Files modified by NOBEL89

Output_Files modified by NOBEL89

Output_Files modified by NOBEL89