User: Anand Rao

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Anand Rao320
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Posts by Anand Rao

<prev • 206 results • page 1 of 21 • next >
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Comment: C: TIN from RSEQC calculated for BAM file using RAW or PROCESSED reads?
... Have to look up my notes, how long is it taking you? Have you tried a test input file and / or contacting the author(s)? ...
written 4 weeks ago by Anand Rao320
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Identifying truncated protein domain encoding DNA sequences
... Is there an off-the-shelf tool or pipeline that will report all protein domain encoding DNA encoding sequences in a given genome, INCLUDING these conditions: 1. the encoded protein domain is partial or truncated, and / or 2. the encoding region may be interrupted by one or more introns, and 3. ...
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Comment: C: SizeFactors for BAM normalization
... I agree - the `plotPCA` and `heatmap` images generated were hard to interpret, I had to use much smaller and meaningful subsets to be able to 'see' anything. Thanks very much for your help. ...
written 12 weeks ago by Anand Rao320
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Comment: C: SizeFactors for BAM normalization
... On a related topic - for `multiBigwigSummary`, is it possible to specify `--bwfiles` and `--labels` as 2 text files containing the respective lists, rather than explicitly at the command line? I have ~ 150 input BW files, so syntax clarity may become an issue, hence this query. This is a very minor ...
written 12 weeks ago by Anand Rao320
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Comment: C: SizeFactors for BAM normalization
... Thank you for confirming _/\\_ ...
written 12 weeks ago by Anand Rao320
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Comment: C: SizeFactors for BAM normalization
... Thanks, Devon. Just to be doubly sure I understood you right, `LibSize` is **not** relevant or factored into the `sizeFactor` value, just the `calcNormFactors` values, yes? (i.e. before it's inverse is used with bamCoverage) ...
written 12 weeks ago by Anand Rao320
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SizeFactors for BAM normalization
... My goal is to make PCA and correlation plots of my RNA-Seq BAM files. Some useful discussion on BioStars such as [this][1], have helped guide my steps. In another post, responding to a question on library size normalization at this BioStars [post][2], user [ATpoint][3] indicates size factor calcul ...
deeptools deseq2 sizefactors bamcoverage written 12 weeks ago by Anand Rao320 • updated 12 weeks ago by Devon Ryan97k
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Comment: C: Time Course RNA-Seq
... My understanding is that your recommended [TimeCourse][1] package seems to have been designed for microarray data, and so loosely - the `voom` [transform][2] in [limma][3] is to ensure RNA-Seq data can be modified to comply with the statistical assumptions underlying microarray data and its analyse ...
written 12 weeks ago by Anand Rao320
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Comment: C: How to find the differences in aligned bam files
... conda install was very fast and easy, thanks [Devon][1]. But I'm confused by your suggestion of RPGC for transcriptome BAMs - because at this [GitHub discussion][2], I thought you instructed that for RNA-Seq BAM files, the normalization type is ideally either RPKM or DESeq2's size factor. No? ...
written 3 months ago by Anand Rao320
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Comment: C: How to find the differences in aligned bam files
... I have `deepTools/2.5.3` installed. When library sizes are quite variable, what is the preferred normalization method of my RNA-Seq BAM files during the [`bamCoverage`][1] step, to convert them to *.bw format for the [`multiBigwigSummary`][2] step - scaleFactor, RPGC or RPKM? Online, however, the 2 ...
written 3 months ago by Anand Rao320

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Popular Question 5 months ago, created a question with more than 1,000 views. For Feeding FASTA-ggsearch36 results for MCL clustering
Popular Question 5 months ago, created a question with more than 1,000 views. For Feeding FASTA-ggsearch36 results for MCL clustering
Scholar 6 months ago, created an answer that has been accepted. For A: REAPR run error
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: mummerplot for genome self alignment NOT yielding full length diagonal graph
Popular Question 8 months ago, created a question with more than 1,000 views. For Feeding FASTA-ggsearch36 results for MCL clustering
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