Open aman-akash opened 10 months ago
I am not sure I can be of great help here as I have never tried to trim PacBio reads before. Trim Galore is specifically meant to be a short-read trimmer with a focus on Illumina read data. I am not sure if Cutadapt itself is capable of trimming PacBio reads, but maybe there is software out there that is specifically designed to work with it?
Read that it worked for some people even with pacbio reads.
Thanks for the clarification.
Cheers.
hmm, maybe it does work but it just takes a long time? I would probably first try it out with a small subset to see if it works in principle, and if it does through some more parallel compute power at it (via -j
). Just monitor the system performance (e.g via top
) to make sure that it is still running....
Hey,
I am trying to trim pacbio sequencing data in a fastq file using trim galore. However, in every run trim galore gets stuck on the trimming step and never goes to the next step. I can see the trimmed file is created and has a relevant size as well. When I checked the run status I saw that the trim galore job had been suspended for over a day.
Any help regarding this would be great. Thank you for making a nice tool.
Cheers, Aman
Command :
trim_galore -q 7 --fastqc --length 1000 -j 4 -o trimmed ../SRR16*****.fastq
I am also attaching the report generated.