BFC and read pairing info¶
There is what I consider a bug in bfc, read pairing information is stipped when using bfc to correct fastQ reads in the Illumina 1.8 format or newer. This has been described here: https://github.com/lh3/bfc/issues/8 and https://github.com/macmanes-lab/Oyster_River_Protocol/issues/2.
The bug requires, assuming you want to interleave and de-interleave reads, which I think most people will want to do, that you place the
/2 tags in the fastQ headers. To do this, follow the below steps.
sed 's_ _/1 _g' file.1.fq > edited_file.1.fq
and to for the /2 read file
sed 's_ _/2 _g' file.2.fq > edited_file.2.fq
Then supply the edited files to seqtk for merging, bfc for correction, and so on...