tigmint-molecule silent about tigmint

[francicco]

Hi Lauren,

Thanks a lot, I solved this some time ago! :) I hope you enjoyed your vacation.
Best,
F

[lcoombe]

Hi @francicco,

Sorry for the delay in getting back to you -- I've been on vacation for the past couple of weeks.

First of all, tigmint expects the barcode to be in the BX:Z tag of your reads -- it looks like you have your reads formatted how older versions of ARCS required the barcode? If you use the reads output from longranger basic, then the barcode will be in the tag where it is expected.

In addition, as you suspected, I think the naming of your reads are preventing the aligner from recognizing that they are paired end with -p. The /1 and /2 suffixes are fine when they are at the end of the read header, but the _<barcode> addition is interfering. I bet that when you specify the R1/R2 separately, it doesn't have to do the smart pairing logic, thus it works better.

Basically, I think if you use the interleaved output file from longranger basic with the barcode in the BX:Z tag, that should solve your issues.

Hope that helps!
Lauren

[lcoombe]

Glad to hear you got it sorted out! :)