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View Code? Open in Web Editor NEW๐ coverage extraction from BAM/CRAM files, supporting targets ๐ ย
Home Page: https://telatin.github.io/bamtocov/
License: MIT License
๐ coverage extraction from BAM/CRAM files, supporting targets ๐ ย
Home Page: https://telatin.github.io/bamtocov/
License: MIT License
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 for real IP regions if we sequence in a single-end mode.
Describe the solution you'd like
Add similar arguments with "--extendReads" from bamCoverage of deeptools would be a very good option.
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. Maybe I am missing something?
To Reproduce
bamtocov EF_V1_S9.MD.sorted.bam --regions Targets_hg38.bed --threads 24 --mapq 20 > EF_V1.cov
Expected behavior
From the paper I gather it should run a lot faster than 6 hours.
System information (please complete the following information):
Describe the issue
bamtocov file.bam
generated "ERROR: coverage went backwards from 0 to 0"
System information (please complete the following information):
Additional context
I do not know what the error means. I generated bam file using minimap2 in Galaxy and I successfully visualized the bam file in IGV.
Thank you in advance.
Describe the bug
When supplying multiple BAMs but no "target", the program has no defined behaviour.
Expected behavior
Should quit erroring
Related to #2
A future release can generate a whole chromosomes target if no target is explicitly provided.
Or provide this option with a dedicated parameter (probably better)
Hi!
I'm trying you strand coverage calculator, using the command:
bamtocov -s alignment.rg.clipped.recalibrated.bam > stranded_cov.txt
But I couldn't found any indication about the strand output, is the first column the forward and the second column the reverse?
Thanks
@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 example, if mate1
of a fragment was recorded as '-' strand in bam, which means that mate1
are actually comes from '+' strand. When setting with --stranded
, mate1
will be counted as '+' strand. My question is, will mate2
of this fragment be automatically counted as '+' strand as well in this case?
Also, will the new '--extendReads INT' parameter also work well with paired-end bam?
Best,
Keren
Hi guys I'm trying to use your tool but every option I try to put return this error. invalid integer: "everything"
I'm using the latest versione 2.7 isntalled with Conda.
First I tried with: bamtocov -w -o -T 24 sorted.bam > coverage.wig
and the error was invalid integer: -o
then I removed -o and I have the error invalid integer: -T
then I tried to write --threads instead of -T and invalid integer: --threads
then I left only the -w and the error was invalid integer: sorted.bam
So after some bestemmie I left only the basic command bamtocov sorted.bam > coverage.bed
and it works.
Is it a common issue for you?
Describe the bug
When specifying --report
but omitting --regions
unconsistent report is produced (dev("t not in index: " & t)
)
Expected behavior
Error and quit
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.
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