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> These formats are terrible for downstream analysis: they are typically not indexed or sorted in a useful way, so it's common to convert them to other formats
by otherme123 4y ago
> These formats are terrible for downstream analysis: they are typically not indexed or sorted in a useful way, so it's common to convert them to other formats (BAM, CRAM), which are optimized for compressing DNA data (and likely exceed zstd in some circumstances).
FASTQ are raw data reads. BAM and CRAM are reads mapped against a genome.
- biotinker 4y agoBAM/CRAM reads are often mapped against a genome, but they needn't be. It's not uncommon in industry to convert FASTQ to unmapped BAM in order to only have a single file format, improve compression, etc.