User: jomo018

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jomo018450
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Posts by jomo018

<prev • 78 results • page 1 of 8 • next >
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Comment: C: FASTQ alignment result is really bad
... Just to put aside anything related with SRA, you can directly download fastq files for your project here: https://www.ebi.ac.uk/ena/data/view/PRJNA389279][1] I have looked at one file and indeed it looks like color-space: @SRR5644749.11183773 11183773/2 T220330222222312020021131122222210 ...
written 2 days ago by jomo018450
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Comment: C: log vs square-root transformation
... Log transform symmetrizes under-expression and over-expression representations. ...
written 29 days ago by jomo018450
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Comment: C: salmon - tximport - deseq2 gene level workflow
... I believe there is contamination on one chromosome (M) which I want to get rid off after alignment but before DE. It's easier to do on the gene level right after `Salmon`. There are other ways to do that, but I thought `tximport` on gene level would be straightforward. ...
written 4 weeks ago by jomo018450
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salmon - tximport - deseq2 gene level workflow
... I am applying `salmon quant` with `--geneMap` option to quantify RNA-SEQ to gene level count files. I plan to proceed with DE using Deseq2. Is it OK to use `txIn` and `txOut` in `tximport` as follows: `tximport(files, type="salmon", countsFromAbundance="no", txIn=T , txOut=T )`. In other wor ...
tximport deseq2 salmon rna-seq written 4 weeks ago by jomo018450
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Answer: A: How to extract unique values between columns in R ?
... Assuming the input structure is cast-ed into a data frame (`df`) by filling `NA`. uu = unlist(df)[ ! duplicated(unlist(df),fromLast=T) & ! duplicated(unlist(df))] apply(df,2,FUN=function(x){r=rep(NA,nrow(df)) ; d=duplicated(c(x,uu),fromLast=T)[1:nrow(df)] ; r[d]=x[d] ; return( r[ ...
written 6 weeks ago by jomo018450
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Comment: C: Mouse Enhancers Database/ Mouse Enhancer annotation
... According to this reference: http://www.statehub.org, H3K4me1 is related to the regulatory function whereas H3K27ac is related to level of activity. ...
written 7 weeks ago by jomo018450
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Answer: A: Mouse Enhancers Database/ Mouse Enhancer annotation
... For enhancer list, consider [http://www.enhanceratlas.org/download2.php][1]. Click **download enhancers** and scroll to mouse tissue for Fibroblast. On page [http://www.enhanceratlas.org/index2.php][2] you can find a short description of their method along with a reference. [1]: http://www.e ...
written 7 weeks ago by jomo018450
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De-duplicate UMI at FASTQ level
... I am looking for a tool to de-duplicate FASTQ files based on UMI which are known per each read. The tool would likely pool identical/similar UMI and check for high similarity between the reads of each pool. The purpose is to reduce processing down the pipeline, in particular to allow mapping of rn ...
umi fastq written 7 weeks ago by jomo018450 • updated 7 weeks ago by i.sudbery2.8k
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Answer: C: TypeError: 'str' object is not callable
... The error and its location indicates that `len` is a string rather than a function. Perhaps `len` was redefined? Something like `len='abc'`. As a side note, notice that `\r\n` will be included in the last field. Consider `column.strip().split(',')`. ...
written 8 weeks ago by jomo018450 • updated 8 weeks ago by RamRS19k
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Comment: C: Error using bedtools "intersect" command
... In addition to @finswimmer response, your sorting scheme is 1, 2, 3. If the gz file is chr1, chr2, chr3, it is probably sorted lexicographically (chr1, chr10). ...
written 8 weeks ago by jomo018450

Latest awards to jomo018

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 8 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 9 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 9 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Why not merging?
Scholar 20 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?

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