User: Anand Rao

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Anand Rao300
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Posts by Anand Rao

<prev • 190 results • page 1 of 19 • next >
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Comment: C: How to find the differences in aligned bam files
... Thanks [Devon][1] (and [krushnach80][2]) - your explanation of why counts would be better for my RNA-Seq data makes total sense. 2 quick follow-up questions: When using counts to obtain PCA and hierarchical clustering, what are typical tools used? And is it normal to use, say only the '100 most hi ...
written 3 days ago by Anand Rao300
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Comment: C: How to find the differences in aligned bam files
... This is an old post, but my question is slightly different - what are the relative pros and cons of using BAM inputs versus count inputs for PCA or multi-cluster to check across RNA-Seq samples (all of them or biol. reps. or whatever)? I can imagine one of the factors being diskspace << coun ...
written 3 days ago by Anand Rao300
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Answer: A: interpreting GC-bias compute and correct results from DeepTools
... Please also see response to a variant of this question at BioConductor from Michael Love at https://support.bioconductor.org/p/132192/ ...
written 6 days ago by Anand Rao300
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Comment: C: interpreting GC-bias compute and correct results from DeepTools
... OK, I see what you mean - SE **OK** for SALMON based **quantification**, but **not** for **correction**. Are there any tools that can visualize and/or correct GC-bias in SE data? May be not, which is probably why you said earlier - > if you do not have PE data then why not considering to simpl ...
written 6 days ago by Anand Rao300
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Comment: C: interpreting GC-bias compute and correct results from DeepTools
... Thank you very much, Devon. ...
written 6 days ago by Anand Rao300
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Comment: C: interpreting GC-bias compute and correct results from DeepTools
... Thanks for that suggestion, I'd never posted there before, but I just [did][1]. Hopefully it's not flagged for cross-posting. You said > Edit2: Rob Patro (salmon author) confirmed in our slack that the > salmon GC bias method is fine with either stranded and unstranded > data, but **paire ...
written 6 days ago by Anand Rao300
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Comment: C: interpreting GC-bias compute and correct results from DeepTools
... From this `ALPINE` [link][1], under **Description:** > It is currently designed for un-stranded pairedend RNA-seq data. My data is un-stranded BUT **single end** RNA-Seq data - so it looks like I cannot use `ALPINE`? Is it because using SE data would violate the underlying (statistical) assumpt ...
written 6 days ago by Anand Rao300
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Comment: C: interpreting GC-bias compute and correct results from DeepTools
... Indeed, I had not realized that Benjamini & Speed algorithm applies only to DNA-Seq. Thanks for pointing that out and for your recommendation for `salmon` using the `--gcBias` flag. So this means computeGCBias itself is not valid for RNA-Seq data, let alone correctGCBias - am I right? Edit: S ...
written 6 days ago by Anand Rao300 • updated 6 days ago by ATpoint36k
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Comment: C: How to merge gff3 files?
... Your request needs to re-worded to reflect the fact that you have one file each for a chromosome - so what you are really looking for is file "concatenation", not 'merging' :) So the answer below is spot on. In the future, if you will need to truly 'merge' GFF3 files, then you can look up - [BEDTO ...
written 6 days ago by Anand Rao300
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interpreting GC-bias compute and correct results from DeepTools
... Greetings! I want to check whether my BAM file suffers from GC-bias, especially because this is a relatively very old sample, with the following details: - Tissue Extraction Kit = GeneAll HybridR+ kit (GeneAll) - RNA Extraction Kit = TruSeq RNA sample preparation kit - Platform = Illumina HiSeq ...
deeptools gc-bias written 6 days ago by Anand Rao300

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Scholar 9 weeks ago, created an answer that has been accepted. For A: REAPR run error
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Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: mummerplot for genome self alignment NOT yielding full length diagonal graph
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