d-j-e

try running makDir.sh via batch outside the pieline and see what happens

Can you send me your config file - if you don't want to post it here, you can send it directly to me via David.Edwards @ monash.edu (remove the spaces)

Apologies for the delay in responding - just got feedback on a paper very close to submission and have had to repeat some of the analysis rather quickly.... There is...

Hi Kesia, Sorry, paper out of way (for now) so can get on to this... You shouldn't need to up the mem to 8GB unless any of your read sets...

Are you running on a torque/qsub system or a SLURM system (or indeed another OS)?

RedDog is actually 'system neutral'; it is Rubra that controls the job submissions to the relevant queue. Though reddog was originally written on a 'qsub' system so it should have...

You could concatenate the genes together into a 'short' GenBank reference - maybe adding twenty to fifty bases up and downstream to each. Reddog uses the 'local sensitive' setting for...

Hi, If running it on a laptop, you need to set 'distributed' to False and install the required packages the once only, just making sure you install them on the...

Hi Rachel, Can you check if the bams are actually being created? Check in the output/temp subfolders - unfortunately, the way the samtools part of the command works is to...

OOPS - didn't mean to close it!!!