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!
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.
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.