error2 about wengan HOT 3 CLOSED

Hi,
You have to split the Illumina reads into two files (forward and reverse) at the moment Wengan do not handle pairs in a single fastq file. You can split your file using the seqkit with:

seqkit split2 -p 2 sample21_pe.unmapped.fq

https://bioinf.shenwei.me/seqkit/usage/#split2

best,
Alex

from wengan.

thanks, that could have worked, but now I have small reads (less than 60 apparently) so it gives that error now and maybe this won't work. Do you know where can I assemble this illumina reads + pacbio clr reads?

thanks again

from wengan.

Hi,
You have to remove any read shorter than 60bp for running WenganD, the other Wengan modes WengaA and WenganM work with reads < 60bp. Seqkit implements a filter by read length.

Best
Alex

from wengan.