Question: Export Consensus Seq.
1
gravatar for Shangool
7.0 years ago by
Shangool10
Shangool10 wrote:

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 alignment samtools igv • 2.5k views
ADD COMMENTlink modified 7.0 years ago by Rm7.5k • written 7.0 years ago by Shangool10
2
gravatar for David Quigley
7.0 years ago by
David Quigley10k
San Francisco
David Quigley10k wrote:

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 COMMENTlink written 7.0 years ago by David Quigley10k
0
gravatar for Shangool
7.0 years ago by
Shangool0
Shangool0 wrote:

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 COMMENTlink written 7.0 years ago by Shangool0

There is a samtools.pl pileup2fq command in samtools

ADD REPLYlink written 7.0 years ago by 2184687-1231-83-4.8k
0
gravatar for Rm
7.0 years ago by
Rm7.5k
Danville, PA
Rm7.5k wrote:

convert pileup2fq consensus fastq to fasta

ADD COMMENTlink written 7.0 years ago by Rm7.5k
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