User: pyKey

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pyKey40
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Posts by pyKey

<prev • 17 results • page 1 of 2 • next >
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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 3 months ago by pyKey40
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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 3 months ago by pyKey40
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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 3 months ago by pyKey40
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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 3 months ago by pyKey40
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SC-RNASeq data mappability with STAR
... Hello all, I wonder what is a "good" percentage of uniquely mapped reads for a single cell in STAR. Currently I get around 50% given that there is a relaxation of number of matched bases (--outFilterMatchNminOverLread 0). Without this, I would get around 30% unique matches and a whole pile of unali ...
star rna-seq written 6 months ago by pyKey40
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Comment: A: What are median and quantile normalization?
... Right! So more explanation: I have a bunch of RNA-Seq experiments and I am performing some simple gene expression comparisons between two conditions (wildtype vs. mutants). Some conditions have at most two replicates. I already TPM normalized all the samples, but for comparisons, another between-sa ...
written 13 months ago by pyKey40
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What are median and quantile normalization?
... Hello everyone, Normally I use TPM for within-sample analysis. Recently I got a suggestion to use Median and Quantile between-sample normalization methods. I noticed that DESeq and Limma packages offer the methods. But... what are they doing? What is the intuition behind them? Thank you all, ...
normalization rna-seq written 13 months ago by pyKey40
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Answer: A: Is Bio.SeqIO.write() sequential for fastq format?
... You are right, the order is preserved. I double-checked everything and found my code's bug : I was addressing a wrong dataframe somewhere along the way! Thank you for the answers, ...
written 19 months ago by pyKey40
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Is Bio.SeqIO.write() sequential for fastq format?
... Hello everyone, Here I try to run this python code for reading fastq records and their associated barcode from a singlae pandas dataframe and writing them simultaneously in a fastq and a text file, to preserve the order between associations. Somehow the order is lost once both files are filled and ...
python fastq bio.seqio rna-seq biopython written 19 months ago by pyKey40
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Comment: C: How To Mask Repeats In Ngs Data.
... Dear JC, I have some very basic questions about how to map reads to the Repbase consensi, Could you please give me details on? - What is a Repbase consensus? Is it distinct for each repeat family? Is it distinct over species? - Where can I find it/them for Human? - Do I build a regular bowtie2 i ...
written 22 months ago by pyKey40

Latest awards to pyKey

Popular Question 6 months ago, created a question with more than 1,000 views. For What are median and quantile normalization?
Scholar 19 months ago, created an answer that has been accepted. For A: Is Bio.SeqIO.write() sequential for fastq format?

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