John Didion

Do you have an example of a library prep that would produce reads with these characteristics?

Cool, thanks. I’ll look into it. If you have a reference for the protocol that would be helpful. > On Aug 7, 2021, at 10:59 AM, lokapal ***@***.***> wrote: >...

Found this - I assume this is standard protocol? https://www.sciencedirect.com/science/article/pii/S1046202318304742 Here they are trimming all reads at the same position (i.e. the `-u` flag of atropos). Is what they suggest...

It would be helpful to be able to reproduce this error. Would you be able to share the first 50k reads from one of fastq files/pairs that caused an error?

I do not know. I've updated the recipe to specify 3.6+ - hopefully that will fix the issue. https://github.com/bioconda/bioconda-recipes/pull/26174

Thanks! I'll try to work on it this week. Please submit a PR if you figure out the solution.

Hi @plijnzaad - writing to BAM is not currently supported, and I'm still debating whether or not to add it. For now you can workaround this by writing SAM to...

This appears to be a problem with your bamfile. When I converted it to SAM and then back to BAM it worked fine (`samtools view TM249_trunc2.bam | samtools view -Sb...

Specifying stdout/stderr is now fixed in develop.

The error is "Malformed BGZF block" so it's not a difference in the contents but with the compression of the data. I will add a new issue to enable the...