User: Gyan Prakash Mishra

Reputation:
0
Status:
New User
Location:
INDIA
Last seen:
1 year, 3 months ago
Joined:
2 years, 3 months ago
Email:
j********@gmail.com

Posts by Gyan Prakash Mishra

<prev • 9 results • page 1 of 1 • next >
0
votes
0
answers
368
views
0
answers
Comment: C: count table generation using summarizeOverlaps
... Thanks Martin I got my answer, gtf is not from same build. ...
written 16 months ago by Gyan Prakash Mishra0
0
votes
0
answers
368
views
0
answers
count table generation using summarizeOverlaps
... Hi, I am using DESeq2 to analyze RNA-seq data In this first step to generate count table I used following code. library( "GenomicFeatures" ) hse <- makeTxDbFromGFF( "Mus_musculus.GRCm38.84.chr.gtf", format="gtf" ) exonsByGene <- exonsBy( hse, by="gene") fls <- list.files( "Bamfiles", ...
deseq2 tutorial written 16 months ago by Gyan Prakash Mishra0
0
votes
1
answers
340
views
1
answers
Comment: C: significance of ChIPseq peak overlap
... I tried to reproduce the same but I am getting different p and p.adjust values   qSample tSample qLen  tLen N_OL   pvalue p.adjust ARmo_1nM GSM1174480_ARmo_0M_peaks.bed.gz GSM1174481_ARmo_1nM_peaks.bed.gz 812 2296   26 0.000999001 0.001998 ...
written 16 months ago by Gyan Prakash Mishra0
0
votes
1
answers
340
views
1
answers
Comment: C: significance of ChIPseq peak overlap
... Oh  sorry about that. I add that additional column manually. Here is the exact output.   qSample tSample qLen tLen N_OL pvalue p.adjust 1 TF1_peaks.bed Irf1_0.peaks.bed 13094 17119 2633 0.00009999 0.00009999 2 TF1_peaks.bed ...
written 16 months ago by Gyan Prakash Mishra0
0
votes
1
answer
340
views
1
answer
significance of ChIPseq peak overlap
... Hi, I am using enrichPeakOverlap of ChIPseeker to find significance of peak overlap. Here is my result of the overlap with no. of shuffle i.e nshuffle=10000 qSample tSample qLen tLen N_OL   pvalue p.adjust TF1_peaks.bed Irf1_0.peaks.bed 13094 17119 ...
chipseeker written 16 months ago by Gyan Prakash Mishra0 • updated 16 months ago by Guangchuang Yu800
0
votes
0
answers
439
views
0
answers
p value for correlation of two bed files
... Hi all, I am comparing two CHIPseq peak bed file by checking overlap and calculating correlation value.suppose if  X coordinates of A overlaps with B then correlation would be X/total coordinates in A. In order to assess if  correlation is significant or not  I think P value is needed. so If anybod ...
chipseq written 2.1 years ago by Gyan Prakash Mishra0
0
votes
1
answers
842
views
1
answers
Comment: C: Analysis of peaks generated from Homer using Diffbind
... Hi Rory , Thank you so much for help ! I changed 'bamreads" to "bamReads' and Its working. Regards Gyan  ...
written 2.3 years ago by Gyan Prakash Mishra0
0
votes
1
answers
842
views
1
answers
Comment: C: Analysis of peaks generated from Homer using Diffbind
... Hi James, Here are the ouputs. output of sessionInfo() > sessionInfo() R Under development (unstable) (2015-07-11 r68646) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C                [3] LC_TIME=en_US.U ...
written 2.3 years ago by Gyan Prakash Mishra0
0
votes
1
answer
842
views
1
answer
Analysis of peaks generated from Homer using Diffbind
... Hi, I have peak file for four different condition without replicate. I converted the text file to Bed file by taking column 2,3,4,8 and 5 which is chr, start, end, score and strand respectively and also removed first 40 line having "#' in the begining. and then created samplesheet "sample.csv" havi ...
diffbind written 2.3 years ago by Gyan Prakash Mishra0 • updated 2.3 years ago by Rory Stark2.1k

Latest awards to Gyan Prakash Mishra

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 322 users visited in the last hour