Is it possible to subsample the especially large files during alignment using Bowtie2 or bwa?

Question

[Dan]

Hello:

The sequencing facility has a robotic error when some of my ATACseq samples were pooled. There is no problem with data quality. But they generated many more reads for those samples than I asked for or expected. Is it possible to subsample the especially large files during alignment using Bowtie2 or bwa? Because the processing time is too long.

Thanks a lot

Answer 1

[Pierre Lindenbaum]

split your fastqs files and process each pairs of fastq in parallel. How Can I Split Paired End Fastq Files

Answer 2

[GenoMax]

You can use reformat.sh from BBMap suite to subsample reads first. seqtk can also be used.

reads=-1                Set to a positive number to only process this many INPUT reads (or pairs), then quit.
skipreads=-1            Skip (discard) this many INPUT reads before processing the rest.
samplerate=1            Randomly output only this fraction of reads; 1 means sampling is disabled.
sampleseed=-1           Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
samplereadstarget=0     (srt) Exact number of OUTPUT reads (or pairs) desired.
samplebasestarget=0     (sbt) Exact number of OUTPUT bases desired.