Using FCS-GX to split/mask internal adaptor sequences

[bndaniel]

Hello,

I have been working on submitting a genome to NCBI, and along with many others have internal contamination by adaptors (as identified by FCS-adaptor). As recommended, I am trying to use the output from FCS-adaptor as an input to FCS-GX to split or mask the internal adaptors. I made a new report.txt file with action "FIX" or "SPLIT" and get "Applied 0 actions; 0 bps dropped; 0 bps hardmasked" back with no modification to the genome. I noticed someone is having a similar issue in issue #66.

I have attached the modified report.txt file - is there any issue with filling columns with "NA"? is there information I am missing? Thanks for the help. Looking forward to seeing a SPLIT or internal trim function in FCS-adaptor soon!

adaptor_contamination_fcsgx.txt