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Search: Posts Made By: nirav99
Forum: Bioinformatics 08-12-2011, 07:23 AM
Replies: 13
Views: 4,165
Posted By nirav99
Hi Daphna, I am assuming that you are...

Hi Daphna,

I am assuming that you are running on Unix/ Linux and you have the latest java compiler. If so, you can follow these steps :

1) Download and untar / (unzip) latest Picard. We need...
Forum: Bioinformatics 03-24-2011, 12:51 PM
Replies: 13
Views: 4,165
Posted By nirav99
Hi Vince, Download and build the java code...

Hi Vince,

Download and build the java code at https://github.com/nirav99/Illumina-pipeline/tree/master/java/FixCIGAR

This should help you.

Nirav
Forum: Bioinformatics 01-11-2011, 11:49 AM
Replies: 13
Views: 4,165
Posted By nirav99
I wrote a simple tool to handle this based on the...

I wrote a simple tool to handle this based on the API provided by Picard. Basically, it is an extension of Picard's CleanSam.jar with the change that if a read has unmapped flag, CIGAR is set to *...
Forum: Bioinformatics 12-15-2010, 09:55 AM
Replies: 13
Views: 4,165
Posted By nirav99
Hi swbarnes2, Yes, we can have picard...

Hi swbarnes2,

Yes, we can have picard continue through these errors by the lenient stringency. But I was wondering what would be the correct way to handle the reads themselves so that no other...
Forum: Bioinformatics 12-15-2010, 08:26 AM
Replies: 13
Views: 4,165
Posted By nirav99
Smile Handling alignments spanning chromosomes boundaries in BWA

Hi All,

When BWA aligns a read that spans over two chromosomes, it sets the flag as "unmapped" but leaves mapping quality (MAPQ) and CIGAR unchanged.

Picard's validator tool ValidateSamFile...
Forum: Bioinformatics 12-15-2010, 06:29 AM
Replies: 15
Views: 7,620
Posted By nirav99
Hi Cliff, TMP_DIR is a command line...

Hi Cliff,

TMP_DIR is a command line parameter for Picard tools.

So, the way to do it would be

java -Xmx4G -jar FixMateInformation.jar I=input.bam O=output.bam TMP_DIR=/home/temp...
Forum: Bioinformatics 12-13-2010, 07:29 AM
Replies: 15
Views: 7,620
Posted By nirav99
Hi Cliff, Please check the disk space where...

Hi Cliff,

Please check the disk space where you are running this. The exception indicates

"Caused by: java.io.IOException: No space left on device"
Forum: Bioinformatics 12-07-2010, 11:13 AM
Replies: 15
Views: 7,620
Posted By nirav99
Picard's command line utility FixMateInformation...

Picard's command line utility FixMateInformation fixes this error.
Forum: Bioinformatics 09-02-2010, 01:41 PM
Replies: 15
Views: 7,620
Posted By nirav99
Smile Error found while mapping Illumina data using BWA

While mapping Illumina data against BWA, I noticed several errors :

ERROR: Record 58, Read name HWI-ST142_0217:1:63:8795:27966#0, Mate negative strand flag does not match read negative strand flag...
Forum: Bioinformatics 08-23-2010, 12:26 PM
Replies: 1
Views: 4,324
Posted By nirav99
Generating a BAM file from Illumina export files in CASAVa 1.7

Hi All,

I am trying to generate a BAM file from Illumina export files.

I used the CASAVA1.7 tool illumina_export2sam.pl. However, the resulting SAM file did not have sequence dictionary of the...
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