User: rohitsatyam102

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Posts by rohitsatyam102

<prev • 118 results • page 1 of 12 • next >
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Comment: C: Retrieve mutation position and ID for a mutation in hgvs format
... Well as a non-python user I didn't like this tool initially but given it's well-written documentation, I was able to follow. Posting an example just in case if someone like me is struggling. I had a NC IG as follows: "NC_000002.11:g.113890610C>T" and I wanted NP IDs for the same ``` ## Initiali ...
written 6 weeks ago by rohitsatyam102260
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Comment: C: What does minoverlap = 1L means?
... Thanks @ATpoint. For the minOverlap takes the number of bases you wish to consider as a valid overlap. So if you have regions of uniform length (say 1000bp) and you wish to consider the overlap with 500bp as significant overlap, one must set the value to 500L.It's your above-mentioned script that h ...
written 8 weeks ago by rohitsatyam102260
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MNAse-Seq Dataset for Different Cancer Types
... Hi Everyone!! I just needed some information related to TCGA dataset. I was wondering if TCGA has MNAseq dataset for different cancer types? Also While checking the ENCODE website I found two widely used MNAse-seq dataset from two cell lines but they are available for hg19. Would you recommend lift ...
#hg38 #bigwig #cancer #mnaseseq sequencing written 10 weeks ago by rohitsatyam102260
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Comment: C: Crucial difference between dexseq and HTSeq-count
... Hi ! Were you able to figure this out? I am also trying to understand in what mode does dexseq python scripts runs HTseq in the background? ...
written 3 months ago by rohitsatyam102260
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Comment: C: DRIMSeq with more than 2 categories in the group
... Hi @poecile.pal Were you able to figure this out? I also have a similar situation. I have data from 5 different layers of a plant (each having 3 replicates) collected at different days of flowering 4, 8, 10, 16. ...
written 4 months ago by rohitsatyam102260
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RNAseq of rice is super weird
... Hi Peeps!! Something has been really troubling me about a public dataset that I am currently working on. The sequencing quality was of course not very great and there were many reads containing runs of As and Ts. What was super weird was when I switched from an older rice genome reference of 2011 p ...
genome sequence rna-seq written 4 months ago by rohitsatyam102260
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What packages/tools are available to use SJ.out.tab file obtained from STAR
... Hi everyone. I have these `Sj.out.tab` files obtained from STAR and am aware that these files contain high confidence collapsed splice junctions. However, I failed to find tools/R packages that take these files as input and help you do some meaningful analysis like differential splicing. Can you po ...
R next-gen sequence rna-seq written 4 months ago by rohitsatyam102260 • updated 4 months ago by brown.annaleigh10
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Comment: C: AGAT - Another Gff Analysis Toolkit
... Wonderful. Indeed they had identical exon start and end and transcript st too. Thanks Jacques. You really saved the day. The AGAT was otherwise smooth and took care of the problems we were previously facing with other converters. Thanks a load again. ...
written 4 months ago by rohitsatyam102260
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Comment: C: AGAT - Another Gff Analysis Toolkit
... Hi Juke34 I am using AGAT for a gff3 to gtf conversion and I saw some of the isoforms removed "28 identical isoforms removed". Why should an isoform be removed, I don't understand especially if gtf has to be used in RNASeq. Will it make any difference in the counts' quantification both for genes an ...
written 4 months ago by rohitsatyam102260
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Comment: C: GO annotation for rice in an R package
... Hi @djyjin Were you able to figure this out? I am experiencing a similar challenge ...
written 4 months ago by rohitsatyam102260

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For Which one to use for ChipSeq replicate comparison: Spearman or Pearson
Popular Question 10 weeks ago, created a question with more than 1,000 views. For What are chromatin states ?
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