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Commentator to
Devon Ryan
99k
Centurion to
smrutimayipanda
▴
10
Popular Question to
Nicolas Rosewick
9.4k
Popular Question to
Maximilian Haeussler
★
1.4k
Popular Question to
lishen0709
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Recent Replies
Comment: samtools coverage usage
by
smrutimayipanda
▴
10
I meant gene coverage.
For example EGFR is the gene found in patient's data and coverage is 100%. So I want to know how to calculate gene c…
Comment: samtools coverage usage
by
lieven.sterck
11k
Please explain what you mean with "100% coverage" ?
Comment: samtools coverage usage
by
smrutimayipanda
▴
10
Yeah I just want to see my variants should cover 100% coverage or atleast 99% coverage
Comment: samtools coverage usage
by
smrutimayipanda
▴
10
I already mentioned the command. I didnt use any option.
Comment: samtools coverage usage
by
lieven.sterck
11k
you can't .
there is no point in putting the per-base coverage in percentage. As others have already asked: what would be for instance 100…
Comment: Statistics of amino acid usage of multiple aligned sequences?
by
Joe
19k
You can't use the above code with Jalview. I was suggesting them as alternatives. Jalview might have some scripting capability (I don't kno…
Comment: samtools coverage usage
by
Lila M
▴
920
This is why I asked first the options you used for it... Anyway, the best option to get the coverage for every single base in a bed file,…
Comment: Validate input file as BED file
by
Lila M
▴
920
An useful tool for reads most of the bioinformatic files is `rtracklayer`, you can use it as `import("yourfile", format="bed")`
Comment: samtools coverage usage
by
smrutimayipanda
▴
10
Thats what I am asking. How do we calculate the coverage in percentage? the coverage covered by variant should be 90-100%, so I am asking t…
Comment: Is it appropriate to resize peak before ATAC/ChIP-Seq differential peak analysis
by
Lila M
▴
920
If you are following a pipeline or package that recommends that, I will do it, just because the the statistic behind the program may needs…
Comment: Is it appropriate to resize peak before ATAC/ChIP-Seq differential peak analysis
by
shangguandong1996
▴
10
That's OK. I am very greatful that some one can talk about this :).
Answer: Exclude non shared SNPs from two datasets with PLINK
by
Nicolas Rosewick
9.4k
plink is very well documented : https://www.cog-genomics.org/plink/1.9/filter#snp
use `--extract` command to extract SNP ID of your choi…
Comment: Adding p value to Vlnplot in Seurat
by
jvbeltran0122
▴
10
Hi @antonioggsousa I tried your code and may I ask about the basis of significance?
Is the significance:
(a) influenced by the number of c…
Comment: samtools coverage usage
by
gb
★
1.9k
If you want to see the finer details of your results you may need to use IGV (https://software.broadinstitute.org/software/igv/). Based on …
Comment: samtools coverage usage
by
smrutimayipanda
▴
10
And I checked this link. If 9.7 is the coverage, that doesnt mean it is 9%. There should be some concept behind it.
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