Biostar (original) (raw)

Segfaults are related to memory, which is what part of the message is telling you. If you are running this job under a job scheduler make s…

The problem was the filename suffix, it's meaningful in how IGV treats the file. It is .pk here, but changed to .bed and it works.

> Any help is appreciated You should consider upvoting and validating (accepting, green check mark) comments/answers you have received on …

Thank you for your detailed reply

- Merge bams - yes. (why do you have so many ?). Merging fastqs before creating bams is easier (cat *.fastq.gz ) than bam merging. - 150…

Without the presence of [**UMI**][1] in data, it would be difficult to say with certainty that a pair of sequences share an identical origi…

I'll agree with GenoMax here. While the approach of bambu shares several methodological underpinnings with methods used for short-read qua…

Data volume is going to depend on the amount of sequencing. Was this a PromethION flowcell? Tool should handle the data as long as you have…

Did you see a recent thread --> https://www.biostars.org/p/9612865/ which delineates standard methods for short-read data. Bambu is meant…

The overall size for all bam files is around 150 GB. Is this common for nanopore and does this tools handle this volume of data? Thanks fo…

How about using `modkit` provided by Nanopore for methylation data analysis: https://github.com/nanoporetech/modkit

Will refer you back to my comment above. Don't be fixated on the Q scores. You don't say what kind of data this is but it may still align f…

Because this question just received an upvote: I used `vt decompose -s` back in the days, but I think bcftools now also makes you choose th…

I have attached the phred score image of my reads, your opinion will be appreciated.