User: crcarroll

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crcarroll10
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c********@fsu.edu

Posts by crcarroll

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Please Explain Window Size and Step Size
... Very clear explanation. Thank you very much for taking the time! ...
written 28 days ago by crcarroll10
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Please Explain Window Size and Step Size
... Hi, In regards to a sliding window analysis, can someone explain and differentiate the concepts of "window size" and "step size"? Thank you ...
alignment mapping sequencing written 29 days ago by crcarroll10 • updated 29 days ago by RamRS25k
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Answer: A: gene_bodyCoverage.py No usable output...why?
... I used gff3ToGenePred followed by genePredToBed tools from UCSC utilities. This outputs a 12-column .bed. geneBody_coverage.py is running so far without error. ...
written 4 months ago by crcarroll10
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Comment: C: Convert .Gff3 File To 12-Column .Bed File
... This is the answer that saved the day for me. Thank you! ...
written 4 months ago by crcarroll10
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Comment: C: gene_bodyCoverage.py No usable output...why?
... I figured something out. I used gff3ToGenePred followed by genePredToBed tools from [UCSC utilities][1] . This outputs a 12-column .bed. [1]: http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads ...
written 4 months ago by crcarroll10
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Comment: C: gene_bodyCoverage.py No usable output...why?
... Right, I knew that. Part of my question included how to convert my gff file from Ensembl to a 12-column bed file. I thought you were then referring to some other format issue. ...
written 4 months ago by crcarroll10
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Comment: C: gene_bodyCoverage.py No usable output...why?
... Why should the bed file not be formatted correctly? I simply downloaded the gfff from Ensemble and used BEDOPS gff2bed < my_file.gff > my_file.bed. ...
written 4 months ago by crcarroll10
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gene_bodyCoverage.py No usable output...why?
... I am trying to use `geneBody_coverage.py -r Homo_sapiens.GRCh38.97.bed -i my_file.sorted.bam -o testOutput` but it generates no results in the output. As soon as I run it, I get a wall of text that looks like this: [NOTE:input bed must be 12-column] skipped this line: Y 26600890 ...
genebody_coverage.py bed gff2bed rna-seq written 4 months ago by crcarroll10

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