Hi all,
We are working on an application in our wet lab where we introduce
random hexamers into our adapters to allow us to differentiate between
PCR duplicates and fragments that were present in multiple copies of
starting material. The workflow for processing the sequence is that
we trim the first and last six bases off of our single-ended reads and
use those bases as our "FP" or "fragment provenance". When we want to
mark the duplicates we only want to mark reads as duplicates if they
align to the same position AND they have the same FP. Reads aligning
to the same position with different FPs should not marked as duplicates.
If I'm not mistaken, I now see in the Picard docs that I can supply a
BARCODE_TAG to MarkDuplicates to mark the duplicates as I describe
above. My question to the group is if it is more appropriate to use
the BC tag, or to use some custom tags to hold the hexamer sequences
associated with each read. I expect that the BC tag should be reserved
for the classical sample multiplexing application (many libraries in a
pool).
If you are still reading I have another question for you:
-Since our reads are single-ended and we have two separate hexamer
sequences (one from each end of the read)...would you recommend
concatenating them into one sequence (perhaps with a delimiter) and
keeping them in one tag, or separating them into two tags? Would there
be any issues in Picard if we have single ended sequencing but supply
two different barcode-like tags?
thanks,
Richard
--
The contents of this electronic mail transmission are intended to be
CONFIDENTIAL and for the sole use of the designated recipient. If this message
has been misdirected, please contact the sender as soon as possible.
------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
