User: wsciekly.maciek

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Posts by wsciekly.maciek

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GO annotation file for hsa genes
... Dear All, I am trying to perform a GO analysis with `Ontologizer` tool. I cannot find any .gaf files with gene-term annotation anymore... http://current.geneontology.org/products/pages/downloads.html At the official website there are only files for protein-term and rna-term associations (for h ...
database go rna-seq written 9 months ago by wsciekly.maciek0 • updated 8 months ago by geneontologyhelp20
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Answer: A: Extract genomic coverage of specific regions from bam file
... The solution is to use `mosdepth` to create position-wise coverages (the output is in bed) and then intersect them with the regions in bed with `bedtools intersect`. ...
written 9 months ago by wsciekly.maciek0
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Comment: C: Extract genomic coverage of specific regions from bam file
... It seems that my solution worked as I wanted it. Just FYI: The mosdepth per-base output head: 1 0 10001 0 1 10001 10010 3 1 10010 10107 5 1 10107 10113 3 1 10113 10119 2 One of the regions of interest from bed files 5 134374371 134390285 UBE2B 0 + ...
written 9 months ago by wsciekly.maciek0
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Comment: C: Extract genomic coverage of specific regions from bam file
... Thanks! I have just checked it out - unfortunately the sample-output.per-base.bed.gz, again, contains information for the whole genome whereas I just want the per-base coverage in bed files... But this is a bed as well... maybe I can use bedtools intersect to intersect it with the original bed with ...
written 9 months ago by wsciekly.maciek0
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Extract genomic coverage of specific regions from bam file
... I have a bed file with regions of interest and a bam file from STAR - aligned RNA-Seq sample. I want to create a small bash script that would result in a txt file that reports position-wise coverage in these regions. I have been playing with bedtools: I intersected the bed and bam and then I put ...
alignment rna-seq written 10 months ago by wsciekly.maciek0
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Comment: C: Bedtools coverage confuses chromosomes
... I have added the command above; Well, it should be but my bed file does not have MT entries... ...
written 11 months ago by wsciekly.maciek0
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Bedtools coverage confuses chromosomes
... I have a problem running bedtools coverage (bedtools v2.26.0 ): my bed file is: 9 137618991 137619028 EHMT1 0 + Y 14056216 14056289 VCY1B 0 + and my Genome File is: 1 248956422 10 133797422 11 135086622 12 133275309 13 114364328 14 107043718 15 101991189 ...
software error alignment rna-seq written 11 months ago by wsciekly.maciek0

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Scholar 9 months ago, created an answer that has been accepted. For A: Extract genomic coverage of specific regions from bam file

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