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Old 04-01-2012, 11:19 PM   #1
ritzriya
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Arrow Evidence file format

Hi all,

I was just going through the files Complete Genomics is providing as deliverables by their Cancer sequencing service.

I downloaded the data from:
ftp://ftp2.completegenomics.com/Canc...2.0.0/HCC2218/

There are two folders - one for normal and one for tumor sample. When I unzip them - I looked at the evidence folder (GS00258-DNA_A03/ASM/EVIDENCE). I found evidenceDnb files for chromosomes 2,5,6,13 and M only. For the same set of chromosomes, we also have evidence Interval files.

Following is my doubt:
1) The remaining chromosomes have only evidence interval files and no evidence Dnb files. Why is it so? What does it mean?
2) According to the CGA tools userguide, evidence Dnb files are to be converted to SAM format. Does this mean that evidence interval files are not meant to be used for this conversion?

Please guide. Thanks in advance.
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Old 04-03-2012, 02:28 AM   #2
gtyrelle
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Did you download all the EVIDENCE files, pt1-6 ? They are separated due to their size. Evidence interval files specify the windows where local de novo assembly was performed, and are not used in the SAM conversion.
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Old 04-03-2012, 02:37 AM   #3
ritzriya
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Quote:
Originally Posted by gtyrelle View Post
Did you download all the EVIDENCE files, pt1-6 ? They are separated due to their size. Evidence interval files specify the windows where local de novo assembly was performed, and are not used in the SAM conversion.
Thanks a lot, Greg. Yes I downloaded the pt-1.tar only. I got your point. :-)
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Old 06-10-2012, 03:23 AM   #4
lambda3388
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Default a little help please

Quote:
Originally Posted by ritzriya View Post
Thanks a lot, Greg. Yes I downloaded the pt-1.tar only. I got your point. :-)
Hi, could you be kind enough to tell me how to convert the evidence files to map (.sam or .bam) format, please?

Thanx.
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Old 06-10-2012, 05:22 AM   #5
gtyrelle
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For evidence files to SAM see here: http://cgatools.sourceforge.net/docs...l#evidence2sam
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Old 06-16-2012, 10:05 PM   #6
lambda3388
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Default evidence2sam errors

I have been using cgatools for evidence to sam conversion for the cancer datasets on CG website.I keep facing segmentation fault error even after using full path for the evidence file location.Sometimes,the is basic_ios::clear error.Could anyone tell me how to get rid of these errors?
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Old 06-21-2012, 02:23 AM   #7
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What is your goal here in doing the conversion ? First paste the full command line you used to run cgatools, along with the full output of the error.
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Old 07-14-2014, 12:36 AM   #8
arsshia
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Hi, can anyone please help me as of how to convert the feature file format to wiggle file format oR GFF format for utilizing gbrowse in plamodb ..
thanx
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