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Forum: Bioinformatics 03-29-2013, 05:58 AM
Replies: 9
Views: 4,749
Posted By qwsqe
"BAM header too large" problem/issue is caused by...

"BAM header too large" problem/issue is caused by the genome file, which you used to make bowtie[12] index. To resolve the issue, clean up the genome file by removing all scaffold sequences that are...
Forum: Bioinformatics 05-08-2012, 05:28 AM
Replies: 4
Views: 2,708
Posted By qwsqe
Hi Arvid, Thank you very much for the help.

Hi Arvid,

Thank you very much for the help.
Forum: Bioinformatics 05-07-2012, 05:31 AM
Replies: 4
Views: 2,708
Posted By qwsqe
Thanks, arvid. To what extend, Bowtie sets the...

Thanks, arvid.
To what extend, Bowtie sets the FLAG to 0x4 for a read, and make the CIGAR field "not abailable". What are the measure and threshold bowtie uses for setting this?

Thanks
Forum: Bioinformatics 05-07-2012, 12:37 AM
Replies: 4
Views: 2,708
Posted By qwsqe
CIGAR field of SAM file from Bowtie alignment

In a SAM file generated from Bowtie, I found one entry has '*' in the CIGAR field. What does this mean, bad alignment?

Thanks
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