cutadpt for PacBio CCS reads?
pengchy opened this issue · 1 comments
pengchy commented
Hi martin,
For PacBio CCS sequence, there exists several categories concatemers related adaptor and primers, as explained in cDNA_primer wiki:
https://github.com/PacificBiosciences/cDNA_primer/wiki/Artificial-concatemers%2C-PCR-chimeras%2C-and-fusion-genes.
This concatemers can be detected by:
- using "-b" parameter of cutadapt, then deal with the "--info-file="
- run cutadapt two times iteratively.
Because the PacBio become more and more popular, the need will grow or a specific tool should be developed.
Best,
pengcheng
marcelm commented
Sorry, forgot about this. Is this still relevant?