User: rotemkat
rotemkat • 10
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Posts by rotemkat
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Comment:
C: depth per position using mosdepth
... the link is actually broken! ...
written 5 weeks ago by
rotemkat • 10
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Comment:
C: depth per position using mosdepth
... Thanks for your help! ...
written 5 weeks ago by
rotemkat • 10
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Comment:
C: depth per position using mosdepth
... Was not aware of that - Thanks!!
(and yes, i'm familiar with samtools, but it's so slow and i have many bam files...) ...
written 5 weeks ago by
rotemkat • 10
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... Hi everyone,
I'm trying to use "mosdepth" in order to get the depth in each position in a bam file i have (of rna-seq data).
I tried to run -
> mosdepth output_file bam_file
and one of the files i get is:
> output_file.per_base.bed.gz
When I open this file i see that actually the depth i ...
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... I have many bam files (containing rna-seq data), and i need to obtain the total coverage in each file.
I tried to use "samtool depth", but since the output is so huge - and i need to sum up all the values there, i was wondering of there's a simpler/faster way to get this value. ...
written 6 weeks ago by
rotemkat • 10
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... Hi,
I have RNA-seq data of cancer patients and their matched normal as well.
I'd like to calculate for each patient the TMB, but I mostly find information about such calculations for Whole Genome/Whole Exome.
Can you advice me what would be the best way to do such calculations?
Thanks ...
written 8 weeks ago by
rotemkat • 10
• updated
8 weeks ago by
Kevin Blighe ♦ 69k
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... it was actually neither - this is RNA-seq data. ...
written 8 weeks ago by
rotemkat • 10
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... Hi,
I want calculate the TMB for each sample in a cohort i'm using.
I have the mutations data in call stats file.
I know that for the calculation i should know the number of non-synonymous somatic, coding, base substitution, per megabase of genome examined, but i'm not sure what data informs about t ...
written 8 weeks ago by
rotemkat • 10
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... Hi,
Is there a way to get the allele frequency of each mutation in dbSNP?
The data I downloaded from here ( ftp://ftp.ncbi.nih.gov/snp/organisms ) does not include it, but maybe there's another source I'm not familiar with? ...
written 8 months ago by
rotemkat • 10
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... Hi,
Is there a way to select which of the optional outputs to be actually produced and saved?
Currently I get 4 files (0000, 0001, 0002, 0003) and I actually need only one of them (the first).
Thanks ...
written 11 months ago by
rotemkat • 10
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For enrichment of transcription factors
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