Hi,
I have been testing the scripts with 10x 5' v1 gene expression libraries. For what I see in the documentation, I applied the following changes:
I specified -fivePbc in the scanfastq step and -p in the assignumis step
I changed the UMI length in the config.xml file to 10bp and the list of barcodes for 737k-august-2016.txt
I was wondering if for this protocol is also necessary to add the option -noPolyARequired in the scanfastq step and maybe change the TSO sequence in some tag of the config.xml, given that it differs to the 3' protocol, as explained in the 10x website?
From ~1 million reads that I demultiplexed independently and I tested, only around 3k got a UMI assign, therefore I was wondering if that would have something to do with some of the protocol specific details
Hi, I have been testing the scripts with 10x 5' v1 gene expression libraries. For what I see in the documentation, I applied the following changes:
-fivePbcin thescanfastqstep and-pin theassignumisstepconfig.xmlfile to 10bp and the list of barcodes for737k-august-2016.txtI was wondering if for this protocol is also necessary to add the option
-noPolyARequiredin thescanfastqstep and maybe change the TSO sequence in some tag of the config.xml, given that it differs to the 3' protocol, as explained in the 10x website? From ~1 million reads that I demultiplexed independently and I tested, only around 3k got a UMI assign, therefore I was wondering if that would have something to do with some of the protocol specific details