Open mblue9 opened 5 years ago
Interesting. I honestly have never heard of stranded-reverse data before, so --stranded
assumes forward orientation, as the -h
flag indicates:
--stranded Is the data strand specific in fwd
orientation? If so, increase speed with this
flag
Maybe the best solution here is to split it into two parameters, --stranded-fwd and --stranded-rev? Alternatively, not using the stranded flag should be fine, depending on the quality and type of data/preparation you have, your mapping rates there aren't the worst-- Whippet is fairly stringent in general.
Ah sorry I hadn't see the fwd
in the help. Thanks for the info. I've run it as unstranded for the moment.
Splitting into 2 parameters --stranded-fwd
and --stranded-rev
could be good as reverse stranded (also known as first strand) is pretty common I think. It's what you get from all dUTP methods afaik including Illumina TruSeq e.g. see here: https://chipster.csc.fi/manual/library-type-summary.html
Hello,
I've been trying out whippet v0.11 with some stranded RNA-seq data and obtained a weird result. With whippet_quant.jl and
--stranded
I get only a small % of reads mapping (~7%) e.g.But if I remove the
--stranded
parameter and then run, I then get a lot more reads mapping e.g. below (although only ~50% not sure if that's lower than expected?). Do you know why that might be?(this is definitely data from a stranded assay and I had checked it previously with Infer Experiment which identified it as stranded reverse)