## User: martin.weihrauch

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1 year, 3 months ago
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2 years, 2 months ago
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m***************@unibas.ch

#### Posts by martin.weihrauch

<prev • 17 results • page 1 of 2 • next >
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... So that is how it works! Thanks for your help. ...
written 16 months ago by martin.weihrauch10
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... Perfect, thanks a lot. ...
written 16 months ago by martin.weihrauch10
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... Thanks, Aaron. Would I use scaleOffset() like this: yoffset <- 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 16 months ago by martin.weihrauch10 2 answers 412 views 2 answers ... 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 ... written 16 months ago by martin.weihrauch10 • updated 16 months ago by Aaron Lun25k 1 answer 284 views 1 answers Comment: C: AveLogCPM of a library subset ... Thank you, everything works flawlessly now. ... written 17 months ago by martin.weihrauch10 1 answer 284 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(fitcounts) %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 17 months ago by martin.weihrauch10
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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 17 months ago by martin.weihrauch10
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... 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 ...
written 17 months ago by martin.weihrauch10 • updated 17 months ago by Aaron Lun25k
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... 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 17 months ago by martin.weihrauch10
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... 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 17 months ago by martin.weihrauch10

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