IanCodes

I would also like to know the answer to this. How is gseGO coded to deal with qvalues in the output?

Is the mm39 blacklist planned, or has it been decided it is not necessary? Thank you.

The epic virtualenv is active, but when I type 'jellyfish' I get: -bash: jellyfish: command not found But it has been installed by pip: 'pip list' shows: jellyfish (0.5.6)

Just bear in mind that you are only analysing reads that map to the transcriptome. I don't think the assumptions made in the lambda background model hold true as you...

Sorry I wasn't clear. MACS2 generates a background model looking within the enriched region, 1,000K and 10,000 from the region, and across the whole genome. However, the transcriptome coverage is...

It is more complicated than mappability, see: https://sites.google.com/site/anshulkundaje/projects/blacklists Although reading the summary suggest they are not applicable to RNA-seq data. But then as these are transcriptome associated reads you might...

Hi @christiane-morecock, In the end I 'liftedOver' the mm10 file to mm39, using the file from 'https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz'. I used a min ratio setting of 0.95 in liftOver. Admittedly, it isn't...