SLOW5 files not working with nanopolish polyA
maximus-sci opened this issue · 2 comments
Hello I'm unable to use slow5 files for polyA calling and was hoping you could help.
I can successfully convert my fast5 files into slow5 and then merge them together using slow5tools.
Indexing with nanopolish also executes with no errors.
When I try to call polyA tail lengths, the script runs with no errors and produces this output:
$nanopolish polya --reads .merged.fastq.gz --bam merged.sorted.bam --genome Reference.cdna.all.fa.bgzf > polyA.tsv
[post-run summary] total reads: 28975, unparseable: 0, qc fail: 365, could not calibrate: 524, no alignment: 56, bad fast5: 0
but in the tsv file, every single read has the qc tag "READ_FAILED_LOAD"
When I try to get tail lengths without converting to slow5, many/most of the reads have the qc tag PASS.
Any advice?
Could you please put the commands you used to convert to blow5 and then the nanopolish commands for using blow5?
@maximus-sci
I think I found the issue and applied a fix which you can find the instructions here jts/nanopolish#967