Bam file format6/9/2023 The smoothest experience would have been if qiime tools import would accept SAM data this would not only be saving one more conversion step (which is annoying but doable, especially when one creates a manifest anyway). The major tripping point that sent me to detours was that conveters ( samtools which I went for, but also bedtools' bamtofastq and picard's SamToFastq as linked in a related post) happily take a bam file that has good (well at least present) metadata on the data being double-ended and throws it out in the default configuration of producing a single fastq file. Having spent way more time than I'd like to admit finding that the data I obtained from sequencing does indeed contain paired reads, I'd like to smooth out road bumps for future users that try to get started from.
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