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Also, the BAM file isn't really the raw file that comes out of the sequencers, that would be FASTA or FASTQ. The BAM file is then, as you stated, what you get a
by JangoSteve 10y ago
Also, the BAM file isn't really the raw file that comes out of the sequencers, that would be FASTA or FASTQ. The BAM file is then, as you stated, what you get after comparing/aligning it to another sequence such as the human reference genome.
- a_bonobo 10y agoSome people have been pushing to use BAM files for unaligned reads too - the upside being that it's a) compressed and b) you know when the file is incomplete as the BAM ending is missing. You don't get that with FASTQ. Most notably, the new versions of the PacBio software produce BAM files with the sequencing reads instead of FASTQ (or h5 as previous versions did)
- rgejman 10y agoYeah, but you can often derive the original FASTQ file from the BAM file anyway so it's like raw data PLUS.