Miten Jain

Hello, Sorry for the delay. Could you tell a little more about the OS and your system so I can try and reproduce the error on our end? Also, we...

Hi @vahidAK , We have an updated version of signalAlign here: https://github.com/UCSC-nanopore-cgl/signalAlign Give it a try and let us know what you think?

Sorry for the hassle. I agree we need to tag our releases in git, and will get this effected shortly. Re: pysam, if your system python has the same version...

Pysam 0.8.2.1 not working is weird. What is the OS on your cluster? I'll try to reproduce the issue on our end if possible.

Hi Felix, Couple of thoughts. 1. Was the virtualenv functional before you had to update pysam? 2. When you say a large size file, how large are you talking about?...

Hello, Yes, the present implementation works only with fastq. It is something we have been intending to fix for some time, since we internally convert fastq to fasta before aligning...

Hello, Sorry for the delay. I'll have that patched up in a couple of days. I'll let you know when done.

Are you using a minimap2 with -ax map-ont settings? And did you remove the secondary and supplementary alignments? marginStats presently works with primary alignments only (and with -ax map-ont setting)....

Yes, marginAlign can chain the alignments to the most contiguous alignment per read. Presently, this only works with the splice unaware alignments (-ax map-ont). Chaining and realignment are enabled by...

Hello, Sorry for the delay in getting back, and for the hassle. We can certainly change the VCF format if the current one is not suitable for downstream processing. Would...