User: martin.weihrauch

Reputation:
10
Status:
New User
Location:
Last seen:
2 months, 3 weeks ago
Joined:
1 year, 1 month ago
Email:
m***************@unibas.ch

Posts by martin.weihrauch

<prev • 17 results • page 1 of 2 • next >
0
votes
2
answers
150
views
2
answers
Comment: C: Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with ed
... So that is how it works! Thanks for your help. ...
written 3 months ago by martin.weihrauch10
0
votes
2
answers
150
views
2
answers
Comment: C: Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with ed
... Perfect, thanks a lot. ...
written 3 months ago by martin.weihrauch10
0
votes
2
answers
150
views
2
answers
Comment: C: Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with ed
... Thanks, Aaron. Would I use scaleOffset() like this: y$offset <- scaleOffset(y = y, offset = t(t(log(normMat)) + o)) # y is now ready for estimate dispersion functions see edgeR User's Guide   Or should I do this: offset <- t(t(log(normMat)) + o) y <- scaleOffset(y, offset) Are you su ...
written 3 months ago by martin.weihrauch10
2
votes
2
answers
150
views
2
answers
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
... I used Salmon for quasi-alignment-based quantification of my RNAseq data (mouse, mm10, raw fastq-files). I imported the generated quant.sf data files into R for use with edgeR, following the manual here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html Here is ...
rnaseq edger salmon tximport written 3 months ago by martin.weihrauch10 • updated 3 months ago by Aaron Lun21k
0
votes
1
answers
140
views
1
answers
Comment: C: AveLogCPM of a library subset
... Thank you, everything works flawlessly now. ...
written 4 months ago by martin.weihrauch10
0
votes
1
answers
140
views
1
answers
Comment: C: AveLogCPM of a library subset
... Perfect, thanks, I will do that. Greatly appreciate your response.   When modifying fit like this:  index <- rownames(fit$counts) %in% lncRNA_subset$V1 summary(index) remain <- rownames(fit$counts)[index] fit$counts <- fit$counts[remain, ]   I get the following error when calling glmT ...
written 4 months ago by martin.weihrauch10
0
votes
1
answers
140
views
1
answers
Comment: C: AveLogCPM of a library subset
... Thank you very much Aaron, I will follow your advice. This helps me greatly, as I was struggling between different approaches, each giving different results keeping me awake at night. I think the lncRNAs should behave the same as protein-coding mRNAs, being poly-adenylated and all. Thus I will go w ...
written 4 months ago by martin.weihrauch10
4
votes
1
answer
140
views
1
answer
AveLogCPM of a library subset
... I've mapped mouse-RNA-Seq data to a genome using the Gencode M17 comprehensive annotation .gtf file. Then I did read-counting using featureCounts, but I supplied a subset of the annotation, containing only lncRNA annotations. This leads to  only 1-2% of all reads to align successfully (usually less ...
rnaseq edger written 4 months ago by martin.weihrauch10 • updated 4 months ago by Aaron Lun21k
0
votes
1
answers
180
views
1
answers
Comment: C: Low number of assigned reads using featureCounts / Strandedness issue
... Hello martin.weihrauch! We believe that this post does not fit the main topic of this site. Issue has been resolved successfully. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us ...
written 4 months ago by martin.weihrauch10
0
votes
1
answers
180
views
1
answers
Comment: C: Low number of assigned reads using featureCounts / Strandedness issue
... I was told that "reverse" strand specificity should only be used when working with paired-end reads. For single-end it should be "stranded" and not "reverse".  So I take it that this was mis-information and using strandSpecific = 2 for "reverse" counting is the correct way when the kit uses the dUT ...
written 4 months ago by martin.weihrauch10

Latest awards to martin.weihrauch

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 275 users visited in the last hour