bamtocov

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add an argument for bamtocov to allow the extension of reads to fragment size from single-end sequencing data

4

**Is your feature request related to a problem? Please describe.** In most of the IP-based methods, we need to extend reads to the fragment size to get the correct coverage...

kerenzhou062

How did bamtocov deal with paired-end bam from stranded libraries?

1

@telatin Dear Dr. Telatin, I'm curious about how `bamtocov` deal with paired-end bam from stranded libraries by setting with `--stranded`. Will `bamtocov` automatically treat mated reads as reverse strand? For...

kerenzhou062

A way to calculate coverage breadth

2

It is often useful to see if reads horizontally cover a certain percentage of a locus' length. Existing tools (bedtools coverage) are too slow/memory-consuming with unsorted BAMs.

BharatRaviIyengar

It will be very useful to add an option "--rpm" to allow users to calculate the Reads per million mapped reads

4

kerenzhou062

`bamtocov` generated "ERROR: coverage went backwards from 0 to 0"

1

**Describe the issue** `bamtocov file.bam` generated "ERROR: coverage went backwards from 0 to 0" **System information (please complete the following information):** - UBUNTU 20.04 app **Additional context** I do not...

ChooseelBunsuwansakul

[BUG] run time exceeds > 6 hours human exome

2

**Describe the bug** Dear bamtocov team, I have human WES data and am trying to run bamtocov. After 6 hours, not even half is done/calculated, even when using 24 threads....

ESDeutekom