User: anu014

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anu014170
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India
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5 days, 22 hours ago
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4 years, 1 month ago
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Posts by anu014

<prev • 152 results • page 1 of 16 • next >
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Comment: C: ChIp-seq RNA-seq overlap
... Thanks a lot Devon for solving the problem! ...
written 8 months ago by anu014170
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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 8 months ago by anu014170
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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 8 months ago by anu014170
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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 8 months ago by anu014170
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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 8 months ago by anu014170
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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 8 months ago by anu014170
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Comment: A: Neoantigen prediction Tools
... Thanks a lot all! I'll try them and get back to you :) ...
written 8 months ago by anu014170
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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 8 months ago by anu014170
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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 8 months ago by anu014170
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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 9 months ago by anu014170

Latest awards to anu014

Popular Question 6 months ago, created a question with more than 1,000 views. For Motif prediction in Chip-seq data
Popular Question 6 months ago, created a question with more than 1,000 views. For Subtracting one BAM [control] from another BAM [sample].
Popular Question 6 months ago, created a question with more than 1,000 views. For GC & AT content calculation
Popular Question 6 months ago, created a question with more than 1,000 views. For Plotting TSS & TTS for Chip-seq peaks
Popular Question 6 months ago, created a question with more than 1,000 views. For Narrow & Broad peaks from 'macs2 bdgdiff'
Popular Question 6 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 Help with Piranha bin size for BED files
Popular Question 6 months ago, created a question with more than 1,000 views. For Chip-seq peak annotation [Chipseeker]
Popular Question 6 months ago, created a question with more than 1,000 views. For Help with Piranha bin size for BED files
Popular Question 6 months ago, created a question with more than 1,000 views. For Subtracting one BAM [control] from another BAM [sample].
Popular Question 6 months ago, created a question with more than 1,000 views. For Chip-seq peak annotation [Chipseeker]
Popular Question 8 months ago, created a question with more than 1,000 views. For CLIPdb bulk download
Popular Question 8 months ago, created a question with more than 1,000 views. For CLIPdb bulk download
Popular Question 9 months ago, created a question with more than 1,000 views. For CLIPdb bulk download
Scholar 10 months ago, created an answer that has been accepted. For A: Plot lines color change in plotAvgProf2 [ChIPseeker]
Popular Question 11 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 Plotting TSS & TTS for Chip-seq peaks
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Popular Question 13 months ago, created a question with more than 1,000 views. For Extension size problem in MACS2
Popular Question 14 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?
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