Jared Simpson
Jared Simpson
is it possible the process ran out of memory? this is the usual cause of this type of error
Thanks. It is hard to say what the problem is. Would you be able to determine which read is causing the problem by running on subsets of the bam?
Hi, Sorry for the slow reply, I was traveling last week. I don't think it is safe to make this change. This checks that the segmentation of the read is...
@nickloman do you explain this in the Ebola/Zika papers?
Hi Nuria, > From what I've understood from another issue I've read, the way that the tool is counting the reads is different. As far as I understood it, Nanopolish...
Could you try: ``` samtools view -F 4 alignments.bam | wc ```
Are you using the latest version of nanopolish?
I still don't know the root cause of this issue but I'd appreciate if you could run 0.14.0 and let me know if you get the same count. Jared
Actually I think it is fixed in 0.14.0. Reviewing the changes between versions, I remember now that there was a double-counting of reads in 0.13.2. It doesn't effect the result,...
Can you check whether the sequencing summary file format is the same for the MinION and PromethION data? Is it possible the split sequencing summary file is truncated (does it...