User: m93

gravatar for m93
m93140
Reputation:
140
Status:
Trusted
Location:
Last seen:
1 week, 3 days ago
Joined:
1 year, 7 months ago
Email:
m***********@gmail.com

Posts by m93

<prev • 50 results • page 1 of 5 • next >
0
votes
0
answers
243
views
0
answers
edgeR: how to make contrasts with makeContrasts
... I am very new to RNAseq analysis and I am learning how to use edgeR to perform differential gene expression. I am quite confused about how contrasts work. According to the manual: > design <- model.matrix(~0+group, data=y$samples) > colnames(design) <- levels(y$samples$group) &g ...
ngs makecontrasts glm edger dge written 3 months ago by m93140
0
votes
0
answers
213
views
0
answers
UCSC hub: autoscale option for multiwig track
... I am making a hub on UCSC Genome Browser and I am aiming to display multiple bigWig files as a single track (multiwig container). I decided to use the autoscale option because I wanted a dynamic scale: y axis changing depending on the maximum values in the current observed window. However, I am con ...
multiwig autoscale track ucsc written 5 months ago by m93140
0
votes
1
answer
215
views
1
answers
Comment: C: variableStep vs fixedStep for range formats
... Thanks, that really helps! ...
written 5 months ago by m93140
3
votes
1
answer
215
views
1
answer
variableStep vs fixedStep for range formats
... I am reading the specifications of many range formats: BED, bigBED, bedGraph, Wig and BigWig. I am having a hard time summarizing which of these can store data that is either variableStep or fixedStep. For each format, there is an important parameter/characteristic to understand: - **Size of the ...
bedgraph ucsc bigwig formats range written 5 months ago by m93140 • updated 5 months ago by RamRS20k
0
votes
0
answers
231
views
0
answers
Comment: C: Reformating bedGraph files in shell script
... Was literally about to add an update with that :) Thanks! ...
written 5 months ago by m93140
1
vote
0
answers
231
views
0
answers
Reformating bedGraph files in shell script
... I have 100 bedGraph files that I need to reformat before converting them into bigWig files for display in UCSC Genome Browser. Briefly: - These bedGraph files were obtained using genomeCoverageBed on bam files (for which the SN tag did not have "chr" in front of the chromosome number). - Since t ...
bedgraph ucsc bigwig chr awk written 5 months ago by m93140 • updated 3 months ago by Biostar ♦♦ 20
0
votes
1
answer
352
views
1
answers
Comment: C: Output bedGraph from genomeCoverageBed is missing "chr"
... What do you mean? The awk command suggested by jared.andrews07 will not work within a script. I'm guessing this is maybe a simpler way than my awk command? I'm not very comfortable changing a BedGraph like this to be honest, I wish there was a way out outputting a bedGraph with what I want directly. ...
written 5 months ago by m93140
0
votes
1
answer
352
views
1
answers
Comment: C: Output bedGraph from genomeCoverageBed is missing "chr"
... I sorted it out I think. I was using this command within a shell script so instead of $0 being the whole line of the bedgraph, it was outputting the name of the script. I used this instead: awk -v LINE="$0" '{print "chr" $LINE}' $BEDGRAPH ...
written 5 months ago by m93140
0
votes
1
answer
352
views
1
answers
Comment: C: Output bedGraph from genomeCoverageBed is missing "chr"
... Yeah it seems to be the case. The BAM headers have the following tags: @SQ SN:1 @SQ SN:2 etc I tried doing this awk command you suggested but can't get it to work in the context of a shell script at the moment. Not sure how to get awk to recognize $0 as the whole line. ...
written 5 months ago by m93140
3
votes
1
answer
352
views
1
answer
Output bedGraph from genomeCoverageBed is missing "chr"
... I am trying to make a UCSC Genome Browser hub using bigWig files. My starting file format are BAM files. Briefly, my script does as follows: - Scale the BAM file according to a specificic pre-determined scaling factor (using samtools). - From scaled BAM, make a bedgraph representing coverage (us ...
bedgraph bigwig genomecoveragebed rna-seq ucsc written 5 months ago by m93140 • updated 5 months ago by RamRS20k

Latest awards to m93

Student 17 days ago, asked a question with at least 3 up-votes. For Any suggestions for basic intro to submitting jobs to an HPC cluster?
Student 5 weeks ago, asked a question with at least 3 up-votes. For Which skills are most required to become a good bioinformatician?
Student 5 months ago, asked a question with at least 3 up-votes. For Which skills are most required to become a good bioinformatician?
Supporter 6 months ago, voted at least 25 times.
Student 8 months ago, asked a question with at least 3 up-votes. For Which skills are most required to become a good bioinformatician?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2258 users visited in the last hour