Tim Sterne-Weiler

Hi @PeterVenhuizen, if you look in src/bam.jl you'll see it's a pretty simple bit of code that's filtering reads for each gene-- ```julia isspliced( rec::BAM.Record ) = ismatch(r"N", BAM.cigar(rec)) strandpos(...

Hey @PeteCausey-Freeman, The refseq annotation file is in refflat format and is actually deprecated. So feel free to completely ignore that file, the current version of Whippet won't read it...

The answer is in #118 "Whippet only accepts as input the standard four-line FASTQ file (described here: https://support.illumina.com/bulletins/2016/04/fastq-files-explained.html). The extra name id after the '+' is the problem. This is...

Hi @limeng12, thanks for opening this. The issue itself is a duplicate of what was reported in the gitter chat by @nick-webster and @DidrikOlofsson. I should already have the files...

Hi @aleighbrown -- Yah I need to address this bug. But, it is probably worth mentioning that the approach of supplementing the index with a bam file makes more sense...

Hi @OlgaVT -- it is on pg. 13 of the Methods S1. "Since the EM-algorithm provides only a point-estimate for Ψ without a depth dependent measure of variance, we utilize...

The probability is derived by simply sampling from both emperical distributions over PSI and comparing the two-- counting the proportion of estimates where X > Y for example.

Hi, there is not currently an easy way to do this, although I agree that this is a necessary label to add to the output, and I plan to do...

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?...

Moved to Whippet v0.4