Question

Export Consensus Seq.

1

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13.6 years ago

Shangool ▴ 10

I want to export my consensus sequence from IGV to look at the reads in BLAST. I could make consensus pileup file by SAMTools but the problem is that I can not convert pileup to fasta or fastq. Could you please tell me, is there anyway to export consensus seq.?

Many Regards

consensus igv samtools alignment • 4.8k views

ADD COMMENT • link updated 13.6 years ago by Rm 8.3k • written 13.6 years ago by Shangool ▴ 10

score 2 · Answer 1 · 2010-09-10

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13.6 years ago

David Quigley 11k

The developer says (as of last year) IGV can't export, and a quick check of the manual seems to confirm this is still true. See this thread on Seqanswers:

http://seqanswers.com/forums/showthread.php?t=6469

Any reason why you can't use SAMtools (or your genotype caller of choice) to do this?

ADD COMMENT • link 13.6 years ago by David Quigley 11k

score 0 · Answer 2 · 2010-09-10

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13.6 years ago

Shangool • 0

HI Tanks for reply. I can not look at my consensus from SAMTOOLS, because it is in pileup format and I can not convert it to fastq and then pt the reads in BLAST. Do you think is there any way?

many tanks

ADD COMMENT • link 13.6 years ago by Shangool • 0

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There is a samtools.pl pileup2fq command in samtools

ADD REPLY • link 13.6 years ago by 2184687-1231-83- ★ 5.1k

Ram · Answer 3 · 2010-09-18

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13.6 years ago

Rm 8.3k

How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?

ADD COMMENT • link updated 4.6 years ago by Ram 43k • written 13.6 years ago by Rm 8.3k