User: m93
m93 • 140
- 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
... 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 ...
written 3 months ago by
m93 • 140
0
votes
0
answers
213
views
0
answers
... 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 ...
written 5 months ago by
m93 • 140
0
votes
1
answer
215
views
1
answers
... Thanks, that really helps! ...
written 5 months ago by
m93 • 140
3
votes
1
answer
215
views
1
answer
... 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 ...
0
votes
0
answers
231
views
0
answers
... Was literally about to add an update with that :) Thanks! ...
written 5 months ago by
m93 • 140
1
vote
0
answers
231
views
0
answers
... 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 ...
0
votes
1
answer
352
views
1
answers
... 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
m93 • 140
0
votes
1
answer
352
views
1
answers
... 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
m93 • 140
0
votes
1
answer
352
views
1
answers
... 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
m93 • 140
3
votes
1
answer
352
views
1
answer
... 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 ...
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?
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Bash: find duplicates based on 2 columns and keep duplicate with lowest value in a different column
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Bash: find duplicates based on 2 columns and keep duplicate with lowest value in a different column
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?
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Bash: find duplicates based on 2 columns and keep duplicate with lowest value in a different column
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