User: hamaor

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hamaor0
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Posts by hamaor

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Comment: C: Error while annotating with Chipseeker
... thanks. I download it and tried using it, please see my comment about it ...
written 9 months ago by hamaor0
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Answer: A: Error while annotating with Chipseeker
... I generated my peaks using MACS2 and a peak file is looks like that: chr start end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name 1 1024833 1025212 380 1024925 26.00 12.93083 5.17873 7.28933 P53_1_peak_1 1 1047480 ...
written 9 months ago by hamaor0
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Comment: C: Error while annotating with Chipseeker
... could you send me the link for the .pl script? thanks ...
written 9 months ago by hamaor0
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Error while annotating with Chipseeker
... I followd the Diffbind pipeline for a ChipSeq data: peaksets2 = dba(sampleSheet="SampleSheet.csv",config = data.frame(RunParallel=TRUE, AnalysisMethod=DBA_DESEQ2, bCorPlot=FALSE, bUsePval=TRUE, minQCth=10),minOverlap = 2) peaksets2 <- dba.count(peaksets2) peaksets2 <- dba.con ...
chip-seq diffbind chipseeker annotation written 9 months ago by hamaor0
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how to retrieve binding affinity matrix in diffbind
... hey everyone, I'm performing ChIP-Seq analysis using diffbind, after doing: > dba.count(peaksets, summits=250) I would like to get the binding affinity Matrix into a text file. help will be highly appriciated!! ...
diffbind dba.count chip-seq written 9 months ago by hamaor0 • updated 8 months ago by Rory Stark550
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Answer: A: High no feature counting when using strand specific data
... I tried it. counting percentage drops dramatically. though samples has high percentage of "no feature" when strand= yes presents more counted reads than others when strand = reverse. ...
written 2.3 years ago by hamaor0
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High no feature counting when using strand specific data
... As i'm analyzing strand-specific RNA-seq data, prepared with Epicenter kit, I used HT-Seq count with the option: -s yes Some of my samples had only ~50% counted reads (the rest is had no feature) while others over 85%. i tried to count again, this time -s no, than all of my samples had over 85% coun ...
count strand specific epicentre rna-seq written 2.3 years ago by hamaor0
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Comment: C: help with Gene Bank annotation and GFF file
... that was extremely helpfull!! i appriciate it! ...
written 2.4 years ago by hamaor0
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help with Gene Bank annotation and GFF file
... Hi everyone, I downloaded one of E.coli's strains fasta file from [here][1]. unfortunately i couldn't find its compatible gff file. in this point if any one can help me find one it could be awsome! I wrote a script converting fasta to gff3 using gene features fasta file found in the same link. most ...
gff genebank rna-seq written 2.4 years ago by hamaor0 • updated 2.4 years ago by h.mon28k

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