User: Sadia

gravatar for Sadia
Sadia50
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1 year, 3 months ago
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4 years ago
Email:
s*******@uottawa.ca

Posts by Sadia

<prev • 27 results • page 1 of 3 • next >
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Comment: C: ngsplot heatmap scale discrepancy
... Thanks for your help! ...
written 18 months ago by Sadia50
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Comment: C: ngsplot heatmap scale discrepancy
... The command I used is the basic one: ngs.plot.r -G mm9 -R bed -C configuration-file.txt -O outputfile.txt I loaded heatmap.RData and it does have the parameters. So thank you for that! Do you know what the difference between flood.q or flood.frac is? My file only contains flood.frac anyways and ...
written 18 months ago by Sadia50
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Comment: C: ngsplot heatmap scale discrepancy
... I'm looking at the code, but I'm not able to tell exactly parameter is used as the cutoff limit. Could you shed some light on this? The function I'm using within the program: https://github.com/shenlab-sinai/ngsplot/blob/develop/bin/ngs.plot.r ...
written 18 months ago by Sadia50
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ngsplot heatmap scale discrepancy
... Hi, I'm using ngsplot to generate a heatmap for ChIP-seq coverage. However, I would like to replot the heatmap myself with the underlying data provided by ngsplot. I'm a bit confused about the scaling though. The heatmap generated by ngsplot has a scale of (0, 0.9) whereas the max value of the hm ...
chip-seq written 18 months ago by Sadia50
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Comment: A: MEME-Chip output lacks motif names
... Thank you Gautier. I was missing the information in the command. ...
written 20 months ago by Sadia50
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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 21 months ago by Sadia50
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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 2.8 years ago by Sadia50
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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 2.8 years ago by Sadia50
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Comment: C: GEO submission for RNA-seq
... Could you make sure or can someone else confirm this as well? ...
written 3.7 years ago by Sadia50
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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 3.7 years ago by Sadia50

Latest awards to Sadia

Popular Question 18 months ago, created a question with more than 1,000 views. For Bedtools - writing to an output files results in empty files
Popular Question 18 months ago, created a question with more than 1,000 views. For GEO submission for RNA-seq
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Bedtools - writing to an output files results in empty files
Popular Question 2.8 years ago, created a question with more than 1,000 views. For What is the difference between MACS version 1.4 and 2.0?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For What is the difference between MACS version 1.4 and 2.0?

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