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smrutimayipanda
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Nicolas Rosewick
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Maximilian Haeussler
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lishen0709
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roalva1
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Recent Replies
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.
Comment: samtools coverage usage
by
smrutimayipanda
▴
10
I used normal samtools coverage input.bam and samtools depth input.bam. Can you please tell me what parameters should I use? if 20% is the …
Comment: Convert UCSC isoform ID to Ensembl transcript ID
by
Maximilian Haeussler
★
1.4k
Sidenote: UCSC is not using these IDs anymore and has moved to Ensembl IDs. See https://genome.ucsc.edu/FAQ/FAQgenes.html#hg19 Also, the UC…
Comment: Needs recommendation - Variant Call from RNA seq data of tumor-normal pairs.
by
field654
▴
20
Thank you so much for you recommendation. I would look deeper into your publication.
Best.
Field
Comment: samtools coverage usage
by
gb
★
1.9k
In case of ```samtools coverage``` it looks like it is a percentage, so 20% (http://www.htslib.org/doc/samtools-coverage.html). If you want…
Comment: samtools coverage usage
by
Lila M
▴
920
Which options did you use? When you ask for help with a specific results, is always better to write the code or pipeline you use. If not, i…
Comment: Is it appropriate to resize peak before ATAC/ChIP-Seq differential peak analysis
by
dariober
12k
> Just like with RNA Seq analysis
I think there is an important difference between RNAseq and ATAC/ChipSeq. In RNAseq genes are given in a…
Comment: Compare gene coverage across group o samples
by
roalva1
▴
80
Dear,
the experiment is exome dna sequencing from tumor and control. I think it is not a good solution to use edgerR, since it disregards …
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