I'm new at this, and I'm trying to do RNASeq. I've done the quality analysis already with fastqc. Now, I'm on the quality control part. I need to use seqtk trimfq or fastx_trimmer to trim the first 5 bases.
The following commands are not working. The seqtk command produces a single output file. The fastx_trimmer command says "writing nucleotides failed: Disk quota exceeded".
I'm doing this on a terminal on OSX to login in to the machine at school.
find *fastq | parallel -j 4 seqtk trimfq -b 5 {} > trimmed_{}
find *fastq | parallel -j 4 --no-notice fastx_trimmer -Q33 -f 6 -i {} -o trimmed_{}
Any suggestions are greatly appreciated! I'd like to do it in parallel since I have approximately 15 .fastq files. After this step I intend to build a hisat index.
"writing nucleotides failed: Disk quota exceeded" Are you sure you have enough space on disk for the output files? Since you say you are using a computer at school it might well be that your user quota is not that big.