thelovelab/rnaseqgene

RNA-seq workflow: exploratory analysis and differential expression

rnaseqgene's Issues

Wrong link and workflow not available for Bioc 3.18

Hi Mike, please check the link at 712f039 -- thelovelab, not thelovelove ;-)

Not sure if this has any consequence causing this: https://support.bioconductor.org/p/9155029/ or whether it simply has not been built for 3.18 yet?

can workflow background address the decoy sequence concept?

I am working through the workflow vignette, and indexing with salmon 1.4.0 and gencode v36

A message is generated during the indexing step

[2021-01-02 16:17:27.119] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode

I will look at the referenced doc, but in case it is relevant perhaps the vignette could be updated to clarify the situation. I know this is out of scope of the vignette per se.

Hi, I have used versions of this tutorial for many years in my class. Thanks! Today when our class of 35 ran through it, 2 students were missing the quants directory in extdata. I tried deleting extdata and then reinstalling airway, but still had the same issue on their computers. Everyone else was fine so I am not sure of the issue

Confusing explanation on time course experiment

The following chunk of code performs a likelihood ratio test, where we remove
the strain-specific differences over time. Genes with small p values
from this test are those which at one or more time points after time
0 showed a strain-specific effect. Note therefore that this will not
give small p values to genes that moved up or down over time in the
same way in both strains.

On the first sentence, should this not be "where we remove
the non strain-specific differences over time? Or otherwise put, the differences over time that are independent of the strain.

Because you go on to say that genes that react in the same way in both strains are do not receive a small p-value.