Fragment size in "detecting discordant reads" step

[GoogleCodeExporter]

Dear Chimerascan authors,

I have paired end reads with ~500 bp library size (as set by the wet-lab) with 
104 per Illumina reads. with this design, I was wondering what the fragment 
size will be for the discordant reads detection. Will that be 500bp? or 
something else?

Also, should I specific the insert size or will the program automatically 
estimate insert size based on initial alignments?

Also, is there any way you could include IGV screenshots 
showing a successful chimera detected by the algorithm?

I am running chimerascan 0.4.3 on 64-bit linux

Thank you.

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Step 6: Discover discordant reads

The realigned reads are searched for evidence of discordant reads. A discordant 
read is currently defined as follows:

   1. The fragment does not align to the genome within user-specified fragment size range (default: 1000bp)
   2. The pair does not align to a single transcript
   3. The pair does not align to different transcripts that share exonic sequences on the same strand. In otherwords, reads that map to different isoforms of the same gene are excluded, as it is not the goal of chimerascan to discover unannotated splicing patterns within a single gene. 

Original issue reported on code.google.com by waib...@gmail.com on 12 Oct 2011 at 9:30

[GoogleCodeExporter]

Hi there --

Chimerascan will automatically estimate the fragment size distribution -- you 
will not need to set these parameters yourself.  If you run chimerascan with 
the "-v" option, the logging output will include statistics on the insert size 
distribution.  You can check these to verify that they match your expectations.

Given that you have a large library size, you may want to increase the fragment 
size threshold to something larger than 1000bp, otherwise you might see a 
greater number of false positive potential fusions arising from fragments 
larger than 1000bp.  You could perhaps try 2000bp and compare with the default 
of 1000bp.

Best regards and good luck.

Original comment by matthew....@gmail.com on 21 Oct 2011 at 8:40

• Added labels: Type-Other
• Removed labels: Type-Defect

[GoogleCodeExporter]

Thank you very much for the answer.

Is there also a way to visualize the chimeras/fusions using the BAMs in IGV
or some other viewer? I have generated the list and would like to
"see" them via alignments as a part of filtering/downselection.

Thanks, once again, for making available this tool.

Amol

Original comment by waib...@gmail.com on 22 Oct 2011 at 5:07

[GoogleCodeExporter]

Thanks for your response -- we are in the process of developing visualizations 
for the chimeric reads.  We appreciate your suggestion that we provide a BAM 
file containing the chimeric reads and agree that it would be very useful.

We will do our best to provide this as soon as possible.

Original comment by matthew....@gmail.com on 2 Dec 2011 at 5:18

• Added labels: Priority-High, Type-Enhancement
• Removed labels: Priority-Medium, Type-Other

[GoogleCodeExporter]

Original comment by matthew....@gmail.com on 11 Sep 2012 at 6:31

• Changed state: Fixed