rjsorr
rjsorr
Replying to myself, and after a bit a playing around, --min_id 25 and --mincluster 20 (default) was the least stringent for my dataset, but not easy to fully establish as...
thanks
Cheers @pirovc ! I'll add/match the read length column and give it a try
see for compatability solution: https://github.com/khyox/recentrifuge/issues/35
Thanks and yes, I see the issue with the html getting worse. Actually, the solution could be to offer a reduced version of all pooled samples but a full version...
Cheers @khyox, gave it a go! worked for one of my datasets. The other unfortunately, is still giving a 360mb html file :)
271 samples with 7 of these being negatives :) ``` rcf -n /media/ubuntu/Elements/reference_genomes/Recentrifuge/taxdump \ -k /media/ubuntu/Elements/NEWPIPELINE_MetaAIR/RAW_DATA/RECENTRIFUGE1819/18 \ -c 7 -o OUTPUT.html -u only -e MULTICSV -s KRAKEN -x 9606 >...
@khyox, running 1.7, but see 1.8 is on conda now :). cheers
btw @khyox, is it possible to get out abundace tabels (post contaminat removal) as output so I can run these through another program? what is the correct command for this?
sorry for the slow reply @khyox, The problem of removing read contaminants based on read classification, as I think I'm now struggling with, is the reliance on databases and their...