Comments (3)
Hi Lauren,
Thanks a lot, I solved this some time ago! :) I hope you enjoyed your vacation.
Best,
F
from tigmint.
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
from tigmint.
Glad to hear you got it sorted out! :)
from tigmint.
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