Intro-to-rnaseq-hpc-salmon
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hbctraining
Hi I want to ask a question about replicates. [samples.xlsx](https://github.com/hbctraining/Intro-to-rnaseq-hpc-salmon/files/5721221/samples.xlsx) I attached a one file for review. In this data set how can I make in model matrix in EdgeR?...
Hi, I have managed to use salmon without any problem to analyse RNA-Seq (transcriptome) reads. However, at the moment I am trying to use it for small RNAs (microRNAs) quantification...
could be useful since we have time, and we refer to various things i.e strandedness, RNA quality during the workshop
Perhaps add a bit more information about the transcript output containing all transcripts in the transcriptome, but some will not be identified due to the fragment's length (300-500bp). Only those...
The default behavior is for Salmon to probe the number of available hardware threads and to use this number. Thus, if you want to use fewer threads (e.g., if you...
this is now running by default in bcbio, we should incorporate it with an explanation why. Also Rory says: "Also, I’ve been turning on quantitate_genome_alignments which uses the STAR alignments...
The DGE lessons have a better explanation - we should incorporate this https://github.com/hbctraining/DGE_workshop_salmon/blob/master/lessons/01_DGE_setup_and_overview.md
instead of moving the results to the new folder, have it go there automatically. we do it in automation anyway
MultiQC accesses the aux folder to report fragment length distribution, wondering if it also would report information if we had added bias correction parameters (results are also in the aux...