These are chat archives for cboursnell/transfuse

29th
Nov 2016
Drew-Oli
@Drew-Oli
Nov 29 2016 11:06
Hi,
Drew-Oli
@Drew-Oli
Nov 29 2016 11:14

...oops, I'm using the transfuse-0.5.0.tar.gz package version and it seems to be running fine. I just thought I'd share a few things I've found trying to get it running (huge caveat - I'm a biologist trying to be a bioinformatician!). Firstly, I got a warning from SNAP "FASTQ file doesn't end with a newline! Failing." - I'm fairly sure this was because my left.fq and right.fq files contained unpaired reads (I was using input read files produced by Trinity --trimmomatic option, which contain paired and unpaired reads). Second, SNAP failed beacause it "Ran out of scoring candidate pool entries". This was resolved by following a post by Richard Smith on a TransRate google group: You'll need to edit the function build_paired_cmd - specifically you want to add a line. Find the line:

cmd << " -omax 10" # max alignments per pair/read

And add a new line after it:

cmd << " -mcp 10000000" # maximum candidate pool size
...Finally, Salmon kept failing when given multiple threads to run on, but seems to be working fine when run on only a single thread. Not sure if any of this is useful, but thought I'd share! Cheers, Drew