That's a neat trick, and I definitely wouldn't have thought of that
approach, so thanks for that!
After I finished writing this out, I realized it was super long. So here
are the questions I'm asking up front, so you can choose whether or not to
read the details. Thanks!
1. How do I output the
On Wednesday, July 31, 2013, Mayank Tandon wrote:
That's a neat trick, and I definitely wouldn't have thought of that
approach, so thanks for that!
After I finished writing this out, I realized it was super long. So here
are the questions I'm asking up front, so you can choose whether or
Exactly. Jennifer's solution for outputting unmapped reads involves
splitting the FASTQ file into basically two FASTA files, one with sequences
and the other with the corresponding quality score string. So, yes, they
would be matched files.
On Wed, Jul 31, 2013 at 4:42 PM, Peter Cock
I was hoping this question had been asked, but I haven't been able to find
it. I want to output the unmapped reads from bowtie as a fastq file for
subsequent mapping to other genomes (i.e. the --un filename option). I
know I can extract the unmapped reads by filtering on the bitwise values in
Hi Mayank,
The best option I know of is to do the following:
1 - obtain the sequence identifiers for the unmapped reads by filter the
SAM file, then cutting them out
2 - convert the original FASTQ file to FASTA - you should get two
output, one for the sequences and one for the quality score
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