User: Sadia

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Sadia40
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1 month ago
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2 years, 5 months ago
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s*******@uottawa.ca

Posts by Sadia

<prev • 23 results • page 1 of 3 • next >
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Comment: A: MEME-Chip output lacks motif names
... Thank you Gautier. I was missing the information in the command. ...
written 4 weeks ago by Sadia40
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MEME-Chip output lacks motif names
... I've installed MEME locally. However, when I run meme-chip the output files do not assign known names to the motifs that were found. I know I am missing the database of motifs, but I'm not sure how to add this. Thank you for your help. ...
chip-seq written 9 weeks ago by Sadia40
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Answer: A: ngsplot - how to plot enrichment across TSSs of a list of genes instead of all T
... Thanks for your reply. I had been doing what you suggested, but I thought I would give it another shot, and it seems to be working now for some reason, but I'll take it :) ...
written 14 months ago by Sadia40
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ngsplot - how to plot enrichment across TSSs of a list of genes instead of all TSSs
... Hi, I'm a frequent user of ngsplot to plot enrichment of my chip-seq datasets across a given list of regions (bed file containing peaks). However, I am now trying to show this enrichment at the TSSs of a specific list of genes but I always get the same output even when I change the list itself. Thus ...
chip-seq written 14 months ago by Sadia40
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Comment: C: GEO submission for RNA-seq
... Could you make sure or can someone else confirm this as well? ...
written 2.0 years ago by Sadia40
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GEO submission for RNA-seq
... Hello, one of the requirements to submit RNA-seq data to GEO is processed files which they describe can be: 1. raw counts of sequencing reads for the features of interest, and/or 2. normalized abundance measurements, e.g., output from Cufflinks, Cuffdiff, DESeq, edgeR, etc. Has anyone submitted R ...
rna-seq written 2.0 years ago by Sadia40
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How can I retrieve the info to recreate this figure for my own data?
... Hi, I'd like to recreate the following figure for my data. I can think of multi-step, longer way to do it, but I wanted to ask if there is a program of tool that might help me create it more efficiently? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4346130/bin/nihms619734f5.jpg "Each curve is the ...
chip-seq written 2.1 years ago by Sadia40 • updated 2.1 years ago by Dan D6.7k
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Has anyone had experience with Q for ChIP-seq peak calling?
... I have been trying to find tools to estimate fragment length for single end ChIP-seq data. I've been able to get some success with Homer's makeTagDirectory and MaSC but I wanted to triple check my numbers with another tool. Q is able to estimate the average fragment length as well as part of its pea ...
chip-seq written 2.3 years ago by Sadia40 • updated 2.3 years ago by Sinji2.8k
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Comment: C: Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analy
... What did you mean by "However, the wig values are continuous and MaSC requires a binary 0 or 1 value, so any value less than 1 need to be set to 0." ...
written 2.3 years ago by Sadia40
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Answer: A: ngsplot flat lines as output
... It turns out I had two peaks in the file starting with chr1_random. The program was able to run after I deleted those two rows. ...
written 2.3 years ago by Sadia40

Latest awards to Sadia

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