User: urjaswita

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urjaswita0
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Posts by urjaswita

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Problem reading Bed file using dba.count in DiffBind
... Thanks Rory! Okay, so it seems to be the issue with Bed alignment file. I am not sure it is the file format or those files in particular, but I converted them in Bam and everything works now. Thanks again for your help! ...
written 7 weeks ago by urjaswita0
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Comment: C: How to select summit size for histone ChiP-Seq in Diffbind
... Thanks so much Rory! ...
written 7 weeks ago by urjaswita0
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Comment: C: Problem reading Bed file using dba.count in DiffBind
... Thanks so much Rory! Please find the output below. Everything seems okay though. I am really stuck at this step and your help is very much appreciated. I can share the data etc. with you if you wish to have a look. Thanks again for your help! > obj <- dba(sampleSheet='liver_H3K27Ac_samples.c ...
written 7 weeks ago by urjaswita0
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Problem reading Bed file using dba.count in DiffBind
... Hi folks, I am having a trouble with dba.count function in diffbind. It fails with warnings but without any specific information. Please see below: > obj <- dba(sampleSheet='analysis_H3K4me3_samples.csv') S1 Eye  A None 1 Bed S2 Eye  A None 2 Bed S3 Eye  B None 1 Bed S4 Eye  B None 2 Bed S5 ...
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How to select summit size for histone ChiP-Seq in Diffbind
... Hi folks, I am new to Chip-Seq analysis hence this may be a basic question. I want to do differential binding analysis using DiffBind on H3K4me3 and HeK4Ac histone peaks called using macs2 in two different conditions. I am following the tutorial and in the count step below they use summits size ta ...
diffbind histone chip-seq summit size written 9 weeks ago by urjaswita0 • updated 8 weeks ago by Rory Stark2.1k
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Comment: A: Error reading kallisto files using tximport for cross species RNA-Seq analysis
... Thanks Michael for your prompt response! It worked when I sorted the genes in the same order. I have 2 quick follow up questions: 1. Are the kallisto abundance estimates sorted in a particular order? 2. Would it affect the DESeq analysis if I sort the genes alphabetically? I suppose the answer to ...
written 5 months ago by urjaswita0
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Error reading kallisto files using tximport for cross species RNA-Seq analysis
... Hi folks, I want to do a comparison of RNA-Seq datasets of same tissues in multiple species. I quantified the RNA-Seq using kallisto and now I want to read the kallisto files using tximport for DESeq2 analysis. My abundance files have identical transcript id for each species but the transcript leng ...
rna-seq tximport kallisto across species written 5 months ago by urjaswita0 • updated 5 months ago by Michael Love14k

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