mbhall88
commented
5 years ago Looking at the code, it needs to be a single file.
Being able to point at multiple reads files would be super handy though. This would save having to concatenate all the fastq files together for the sake of just binning.
For now I would just do something like the following:
reads_dir=workspace/
cat $(find $reads_dir -name '*.fastq') > tmp_reads.fastq
deepbinner bin \
--classes classifications \
--reads tmp_reads.fastq \
--out_dir .
rm tmp_reads.fastq
For --reads, can I point to the fastq directory output by the minKNOW program? I have multiple fastq files output from basecalling by minKNOW, and I get an error saying that the directory can't be found. Thank you!