Matt MacManes
Matt MacManes
I see that the info is output in an unstructured way on the stout, but for those of us that would like to do some other types of viz, it...
ENHANCEMENT: I'd like to be able to use kallisto as such: ``` seqtk mergepe read1.fq read2.fq | skewer | kallisto quant -i - ``` basically, moving from raw reads, through...
Enhancement: Add gene names from blast results along with other metadata. Would be great to add some working code to the getting started page. For people not sure familiar with...
Camille, I'd like to make a request that ANY version of BUSCO be acceptable. I know this is a PITA the way the py scripts in BUSCO 1.x are named....
Having an issue with the hmmscan part of the run ``` Some tasks failed![dammit.annotate:ERROR] TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm[dammit.annotate:ERROR] Command error: 'cat good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep | /usr/bin/parallel --round-robin --pipe -L 2 -N 10000 --gnu...
Camille, I want to retain all contigs for which _any_ annotation data exists, including BUSCO hits. This would be easy if the BUSCO results were including in the final gff3...
not sure how hard this would be to implement: Currently get a seg fault. ``` paladin align -t 4 -u 2 data/uniprot_sprot.fasta
In your experience, what Bloom filter A error rate is achievable - 0.05, more, less? Should I attempt to optimize parameters such that error rate is minimized - if so,...
Li: Enhancement: Accept interleaved reads with `-i` or `--interleaved`. I'd like to do this: ``` seqtk mergepe $HOME/reads/kidney.1.fq.gz $HOME/reads/kidney.2.fq.gz \ | skewer -l 25 -m pe --mean-quality $trim --end-quality $trim...
Hi: Error in the 2-ovlp stage. Several of the chunks finish successfully (14 of 24), and several of them (10 of 24) fail as per the attached logs. I'm running...