Mapping SRA files without unpacking?
Hi,
Is it possible to submit SRA files for alignment directly to short read aligners like Bowtie, avoiding the intermediate step of unpacking data to fastq?
Thanks!
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As of version 2.3.5 bowtie2 now supports aligning SRA reads.
Prepackaged builds will include a package that supports SRA.
Use as follows
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]
bowtie v.1x
does not support input of SRA accessions.
Read more here: Source link