User: Prakash

gravatar for Prakash
Prakash1.5k
Reputation:
1,490
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Location:
India
Twitter:
gprakash047
Last seen:
15 hours ago
Joined:
4 years, 1 month ago
Email:
j********@gmail.com

Posts by Prakash

<prev • 122 results • page 1 of 13 • next >
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Comment: C: Motif analysis from H3K27ac ChIPseq broad peaks
... Thanks @Venu for your insight. This was helpful. The reason using `broad` option is that histone acetylation marks covers broad regions (~1kb). I tried calling both using `narrow` and `broad` options, in my case also the narrow peaks seems working well. As per your suggestion i can use narrow peaks ...
written 5 days ago by Prakash1.5k
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Motif analysis from H3K27ac ChIPseq broad peaks
... Hi all. Recently, I got sequence for H3K27ac ChIP-seq data performed in various stimulation and knockdown condition. I have processed the reads and did peak calling using macs2. Looking into IGV browser, the enrichment looks good and the peaks are identified. The peaks called are of in the size ran ...
next-gen chip-seq written 5 days ago by Prakash1.5k
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Answer: C: How to process RNA-seq data for a heatmap in R
... If you have not performed differential gene expression, I would suggest using [DESeq2][1] to identify differentially expressed (DE) genes between your KO and control sample. You can filter the list based on fold-change and adj-pvalue. To make a heatmap of DE, you could use rlog or vst value obtained ...
written 15 days ago by Prakash1.5k
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Comment: C: STRING does not support networks larger than 2000 nodes.
... Have you tried using [StringApp][1] in Cytoscape. That should work. [1]: http://apps.cytoscape.org/apps/stringApp ...
written 16 days ago by Prakash1.5k
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Answer: C: how to create a gene co-expression network?
... you need to have a gene expression matrix and you can create co-expression network using WGCNA. https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ ...
written 21 days ago by Prakash1.5k
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Comment: C: Delete character from sequence id
... yes I agree Ram, Here `.` may match anything. to make it more reliable we can use `\.` instead. Thanks ...
written 4 weeks ago by Prakash1.5k
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Comment: C: Delete character from sequence id
... I would try simply `sed 's/_[A-Z].[0-9]*.[0-9]//g'` myfile.fasta ...
written 4 weeks ago by Prakash1.5k
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Comment: C: Cuffdiff - Error in running cuffdiff by using the merged transcriptome assembly
... See below link regarding deprecation of Tophat2-cufflink-cuffdiff https://www.biostars.org/p/309059/ https://www.biostars.org/p/319077/ https://www.biostars.org/p/261273/ ...
written 5 weeks ago by Prakash1.5k
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Answer: A: transformed read counts in deseq2
... you can also extract normalized read count from `dds` object res <- as.data.frame(counts(dds, normalized=TRUE)) ...
written 5 weeks ago by Prakash1.5k
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Comment: C: Using rmats on bioconda
... I think your question is not directly related to bioinformatics. However, I would try `which python` . If python is available from your bioconda --> `~/anaconda3/bin/python`, then command will run otherwise no. Then you may need to do `conda activate` ...
written 7 weeks ago by Prakash1.5k

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Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
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Appreciated 20 days ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
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Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
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Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
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