Mapping SRA files without unpacking?
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6 weeks ago
biostart ▴ 360

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!

alignment Bowtie SRA sequencing • 236 views
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6 weeks ago
GenoMax 109k

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.

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Wonder whether this still works after NCBI moved the SRA repo to the cloud. @OP, I personally would just get the fastq files, NCBI tools are sometimes prone to connection losses and that might kill your job. Just visit sra-explorer.info to get download links for the fastq files, that takes a few minuntes and saves headaches. Servers were a bit slow the last days, maybe this is still an issue and you have to retry download next week.

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