Dear All
I use 50x illumina reads to correct Pacbio reads. about half of raw base were left. for example, the raw Pacbio reads is ~ 20x coverage, the corrected reads is ~10x coverage. Does anybody know why so many base discarded? Thank you very much.
Best,
Wenbo
Hi,
A throughput of 50% is not unexpected when correcting with Illumina data. We typically see somewhere in the 50-65% throughput. The PacBio reads are split when there is no support from Illumina data or other PacBio reads. Any resulting split reads less than 500bp are trimmed. The reads are also trimmed based on final consensus quality to remove any low-error bases. You can also try ECTools to see if you get better throughput on your data.
Sergey
[Bri removed quoted email]
Last edit: Brian Walenz 2015-02-02
Closed, question answered.