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.
Mapping SRA files without unpacking?
1 answer
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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