User: Prakash

gravatar for Prakash
Prakash1.8k
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India
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gprakash047
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Joined:
4 years, 7 months ago
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Posts by Prakash

<prev • 142 results • page 1 of 15 • next >
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Comment: C: GSEA/fold change for ChIP-seq
... Apart from peak calling and annotation, ChIPseq data can also be used to find differential genomic regions across conditions. [DiffBind][1] performs such kind of analysis that internally uses [DESeq2][2] for differential analysis. Similar to raw count for genes, Diffbind extracts raw counts for geno ...
written 1 day ago by Prakash1.8k
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Comment: C: bedGraphToBigWig file converter
... This GitHub post might be helpful for you. https://github.com/taoliu/MACS/wiki/Build-Signal-Track ...
written 2 days ago by Prakash1.8k
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Comment: C: How to cat fastq files but keep different samples separate
... I agree with you [ATpoint][1], paired-end data R1 and R2 should be kept separate. Thanks for highlighting this point. Few things are still no clear to me such as > no overlap between forward and reverse reads > merged reads are not required also as Joe highlighted > difference between ...
written 4 days ago by Prakash1.8k
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Answer: A: How to cat fastq files but keep different samples separate
... $f used in output will create output for each line. you need to try : for f in Sample1_C*.fastq.gz; do cat $f > Sample1_C_merged.fastq.gz; done for f in Sample1_L*.fastq.gz; do cat $f > Sample1_L_merged.fastq.gz; done ...
written 4 days ago by Prakash1.8k
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Answer: C: MACS for a paired-end sequencing
... If it is paired-end fastq file then why you have separate bam files?. The best would be to realign the paired-end data and you will have one bam file and that can be used for peak calling. ...
written 6 days ago by Prakash1.8k
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Comment: C: GRanges intersect and setdiff doesn't add up
... What is total number of genomic regions in treated here? ...
written 21 days ago by Prakash1.8k
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Comment: C: Macs2 output shows only single basepair peak instead of a section of DNA
... Maybe you are looking only peak summit. ...
written 8 weeks ago by Prakash1.8k
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Comment: C: Error on WGCNA. Can't be done with characters?
... I would suggest to follow this tutorial. https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ You need to have expression data for WGCNA analysis. ...
written 9 weeks ago by Prakash1.8k
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Comment: C: Error on WGCNA. Can't be done with characters?
... the datExpr might have column having character values, probably the gene symbol? could you post head() of the datExp ...
written 9 weeks ago by Prakash1.8k
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Comment: C: how to get RNA-binding proteins in mouse
... Just check this database ..This might help http://cisbp-rna.ccbr.utoronto.ca/ ...
written 9 weeks ago by Prakash1.8k

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Student 7 weeks ago, asked a question with at least 3 up-votes. For Motif analysis from H3K27ac ChIPseq broad peaks
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