User: pyKey

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pyKey50
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Posts by pyKey

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bedtools genomecov per-base report in igv
... Hi All, Is there a way to transform the per-base report of an alignment file into igv-readable format? Original command: bedtools genomecov -d -ibam sample_file > out_file Thank you, ...
bedtools per-base report igv written 7 months ago by pyKey50 • updated 7 months ago by ATpoint35k
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Answer: A: Count matrix from bigwig files - Application
... Update. Hope this helps. After looking more closely into multiBigwigSummary: read counts in each region are averaged over the number of bins. Meaning that the end score is dependent on the gene length. After normalizing gene counts from the original bam by length, now the correlation score is 0.95. ...
written 7 months ago by pyKey50
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Comment: A: Count matrix from bigwig files - Application
... Hi All, So I ran multiBigwigSummary on the bigwig file. As follows: 1. Prepared a BED file which contains just "gene" entries from the original gff file. 2. Ran the above given this BED file. 3. Got an outout BED with "gene" coordinates and a count column. 4. Mapped the coordinates of ...
written 7 months ago by pyKey50
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Comment: C: Count matrix from bigwig files - Application
... Thank you a lot for this hint. I would do as you suggested. ...
written 8 months ago by pyKey50
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Comment: C: Count matrix from bigwig files - Application
... Not sure if it is a good idea either, nevertheless, some people seem to do that [Here][1] . Just that, there is no code published. [1]: http://jtleek.com/protocols/bigwig_gene_counts/ ...
written 8 months ago by pyKey50
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Count matrix from bigwig files - Application
... Hi All, Does anyone know a software that can calculate gene count matrix from a bigwig file? Preferred Python. Thanks, ...
seq gene expression bigwig python written 8 months ago by pyKey50
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Comment: C: Per-base coverage to bedgraph or bigwig
... Exactly! My question is that if I construct a file like this: I 1 1 0.5 I 2 2 1.0 I 3 3 1.0 I 11 11 3.5 I 12 12 3.5 I 13 13 3.5 I 14 14 4.0 I 18 18 5.5 I 19 18 5.5 out of the previous one, would it be correct, or d ...
written 16 months ago by pyKey50
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Comment: C: Per-base coverage to bedgraph or bigwig
... Thanks Devon Ryan, Gautier Richard's sample looks like what I get from "bedtools genomecov -bg". That I can easily imitate in my existing file. I am not sure though if it is fully compliant with the definition of bedgraph files from bedtools site: "Whereas the -d option reports an output line desc ...
written 16 months ago by pyKey50
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Comment: A: Per-base coverage to bedgraph or bigwig
... Hey, The format is the regular per-base coverage: I 1 0.5 I 2 1.0 I 3 1.0 I 11 3.5 I 12 3.5 I 13 3.5 I 14 4.0 I 18 5.5 I 19 5.5 I 20 6.0 I 21 6.0 Just that I cannot simply get it from samtools depth nor by bedtools genomecov (which would make ...
written 16 months ago by pyKey50
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Per-base coverage to bedgraph or bigwig
... Hi, I am trying to turn my customized per-base counts of a bam file into bigwig format. From a bedgraph seems there is already a tool : bedGraphToBigWig. Is there already a tool which turns a per-base coverage report to bedgraph format? Thank you, ...
bedtools bigwig bam coverage written 16 months ago by pyKey50

Latest awards to pyKey

Popular Question 16 months ago, created a question with more than 1,000 views. For What are median and quantile normalization?
Popular Question 19 months ago, created a question with more than 1,000 views. For What are median and quantile normalization?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Is Bio.SeqIO.write() sequential for fastq format?

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