User: rotemkat

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rotemkat10
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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 rotemkat10
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Comment: C: depth per position using mosdepth
... Thanks for your help! ...
written 5 weeks ago by rotemkat10
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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 rotemkat10
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depth per position using mosdepth
... 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 ...
mosdepth rna-seq depth written 5 weeks ago by rotemkat10 • updated 5 weeks ago by ATpoint44k
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Obtaining coverage for rna-seq data
... 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. ...
bedtools variant calling samtools rna-seq written 6 weeks ago by rotemkat10
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Can RNA-Seq be used for TMB calculation?
... 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 ...
tmb rna-seq written 8 weeks ago by rotemkat10 • updated 8 weeks ago by Kevin Blighe69k
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Comment: C: how to calculate TMB from call stats file
... it was actually neither - this is RNA-seq data. ...
written 8 weeks ago by rotemkat10
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how to calculate TMB from call stats file
... 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 ...
mutations written 8 weeks ago by rotemkat10
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allele frequency in dbSNP
... 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? ...
dbsnp mutations written 8 months ago by rotemkat10
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bcftools isec outputs
... 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 ...
bcftools written 11 months ago by rotemkat10

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Popular Question 11 months ago, created a question with more than 1,000 views. For enrichment of transcription factors

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