User: anu014

gravatar for anu014
anu014160
Reputation:
160
Status:
Trusted
Location:
India
Last seen:
3 months, 1 week ago
Joined:
3 years, 10 months ago
Email:
a****************@gmail.com

Posts by anu014

<prev • 152 results • page 1 of 16 • next >
0
votes
3
answers
2.1k
views
3
answers
Comment: C: ChIp-seq RNA-seq overlap
... Thanks a lot Devon for solving the problem! ...
written 5 months ago by anu014160
0
votes
3
answers
2.1k
views
3
answers
Comment: C: ChIp-seq RNA-seq overlap
... Or I'll remove --perGroup option and create the graph like this : https://www.dropbox.com/s/gw0rc9jgsq09e69/trial1.pdf?dl=0 and then it can be compared? ...
written 5 months ago by anu014160
0
votes
3
answers
2.1k
views
3
answers
Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon, I was wondering, will using either reference-point or scale-regions in computeMatrix for both chipseq n rnaseq data will work? ...
written 5 months ago by anu014160
0
votes
3
answers
2.1k
views
3
answers
Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon, I took common rows between exon.bed and transcripts.bed and ran remaining commands : computeMatrixOperations cbind -m peaks_sorted_matrix1 rna_16hr_sorted_matrix1 -o output1.mat.gz plotProfile --matrixFile output1.mat.gz --outFileName trial.pdf --samplesLabel peaks rna_16hrs ...
written 5 months ago by anu014160
0
votes
3
answers
2.1k
views
3
answers
Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon, But what if I have different/extra row in exon bed file (like this one : Chromosome 10072 10148)? Should I discard them? Won't I'll be losing data then? FYI, I am using exon file with RNA-seq data and transcript file with Chip-seq data. ...
written 5 months ago by anu014160
0
votes
3
answers
2.1k
views
3
answers
Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon , below are the commands and the bed files I used : computeMatrix scale-regions -S rna_16hr_sorted.bw -R m.sme_exons.bed --metagene -a 500 -b 500 --outFileName rna_16hr_sorted_matrix computeMatrix reference-point -S peak_sorted.bw -R m.sme_transcript.bed -a 500 -b 50 ...
written 5 months ago by anu014160
0
votes
3
answers
738
views
3
answers
Comment: A: Neoantigen prediction Tools
... Thanks a lot all! I'll try them and get back to you :) ...
written 5 months ago by anu014160
0
votes
0
answers
334
views
0
answers
Comment: C: Integration of Chip-seq and RNA-Seq data
... Thanks AT for suggestion. Certainly, the question requires more info. I'll update it soon. ...
written 5 months ago by anu014160
0
votes
3
answers
2.1k
views
3
answers
Comment: C: ChIp-seq RNA-seq overlap
... Hello Devon. I followed the steps from 1-3. Now, I'm stuck at step 4. Below is the command I ran : computeMatrixOperations cbind -m peak_sorted_matrix rna_16hr_sorted_matrix -o output.mat.gz Error : Traceback (most recent call last): File "/home/anupriya/.local/bin/computeMatrixO ...
written 5 months ago by anu014160
2
votes
0
answers
334
views
0
answers
Integration of Chip-seq and RNA-Seq data
... Hello Biostars, Hope you all are doing well! Can someone suggest me any tool other than BETA to integrate RNA-Seq data (from cuffdiff) and Chip-seq data (MACS2 peaks.xls) ? I saw a lay method here (using venn diagram) but I want something more technical - https://geneviatechnologies.com/blog/int ...
next-gen chip-seq rna-seq written 6 months ago by anu014160

Latest awards to anu014

Popular Question 3 months ago, created a question with more than 1,000 views. For Help with Piranha bin size for BED files
Popular Question 3 months ago, created a question with more than 1,000 views. For Subtracting one BAM [control] from another BAM [sample].
Popular Question 3 months ago, created a question with more than 1,000 views. For Chip-seq peak annotation [Chipseeker]
Popular Question 5 months ago, created a question with more than 1,000 views. For CLIPdb bulk download
Popular Question 5 months ago, created a question with more than 1,000 views. For CLIPdb bulk download
Popular Question 6 months ago, created a question with more than 1,000 views. For CLIPdb bulk download
Scholar 6 months ago, created an answer that has been accepted. For A: Plot lines color change in plotAvgProf2 [ChIPseeker]
Popular Question 8 months ago, created a question with more than 1,000 views. For Extension size problem in MACS2
Popular Question 8 months ago, created a question with more than 1,000 views. For Plotting TSS & TTS for Chip-seq peaks
Popular Question 8 months ago, created a question with more than 1,000 views. For How to create 12.8 billion unique alphanumeric strings of length ranging from 2-6?
Popular Question 9 months ago, created a question with more than 1,000 views. For How to create 12.8 billion unique alphanumeric strings of length ranging from 2-6?
Popular Question 10 months ago, created a question with more than 1,000 views. For Extension size problem in MACS2
Popular Question 11 months ago, created a question with more than 1,000 views. For How to create 12.8 billion unique alphanumeric strings of length ranging from 2-6?
Centurion 16 months ago, created 100 posts.
Voter 19 months ago, voted more than 100 times.
Supporter 2.3 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 665 users visited in the last hour