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cutadpt for PacBio CCS reads? #120

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pengchy opened this issue Apr 17, 2015 · 1 comment

pengchy commented Apr 17, 2015

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

Owner

marcelm commented Nov 2, 2016

Sorry, forgot about this. Is this still relevant?

marcelm closed this as completed

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