4 ms·
Generally I thought this was a great piece. I was a little annoyed that he kept referring to "BAM" files as holding his genomic information. e.g.: "He wanted to
by rgejman 10y ago
Generally I thought this was a great piece. I was a little annoyed that he kept referring to "BAM" files as holding his genomic information. e.g.: "He wanted to get his own BAM file and study it."
BAM is just a format that describes the way that short chunks of DNA are aligned to a reference file of other DNA. It would be a BAM file whether you are talking about someone's genome or an experiment where the readout was a sequencing assay.
To hear how off that sounds, consider the following: "He wanted to get his own m4a file to listen to it."
"She wanted to get her own xlsx file to calculate her expenses"
Perhaps its a small gripe, but why not just say "raw data" or "genomic sequence" either of which would be more accurate and not cause some of us to cringe!
- JangoSteve 10y agoAlso, 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.