Re-run Salmon alignment with --gcBias flag

[laurahspencer]

In reviewing vignettes for software that I'm using to analyze the RNASeq data I came across the suggestion to include the --gcBias flag when running Salmon. See this excerpt from the tximport vignette that I'm using to summarize salmon alignments to estimated gene counts:

"A tutorial on how to use the Salmon software for quantifying transcript abundance can be found here. We recommend using the --gcBias flag which estimates a correction factor for systematic biases commonly present in RNA-seq data (Love, Hogenesch, and Irizarry 2016; Patro et al. 2017), unless you are certain that your data do not contain such bias."

@ggoetznoaa it doesn't look like that was used when you ran Salmon, and in looking at the MultiQC report there could be some GC bias happening, so could you re-run Salmon with that flag? See this GitHub for the last Salmon run with inputs that we opted to use.

[ggoetznoaa]

@laurahspencer Done, where do you want me to put the results, script and log files?

[laurahspencer]

Results and log files can go here: https://github.com/laurahspencer/DuMOAR/tree/main/results/salmon
Script can go here: https://github.com/laurahspencer/DuMOAR/tree/main/scripts

Thanks!

[ggoetznoaa]

@laurahspencer Ok, the script is located here: https://github.com/laurahspencer/DuMOAR/blob/main/scripts/run.salmon.align.all_original.megan6_trinity_assembly.gcbias.sh

The results is located here: https://github.com/laurahspencer/DuMOAR/tree/main/results/salmon/all_original.megan6_assembly.gcbias

[laurahspencer]

@ggoetznoaa can I get access to these alignment files?

[ggoetznoaa]

@laurahspencer by default salmon doesn't save mapping information (SAM or BAM files for example). I can re-run salmon with the --writeMappings and possibly --writeUnmappedNames, not sure if the first option will save the information about reads that don't map. Do you want me to re-run salmon? if so which specific salmon runs do you want me to do?

[laurahspencer]

I'll get back to you!