Chromap for processing the complex barcodes in two paired reads

[lin-zhongbao]

Hi! Thanks for updated the --read-format option to accommodate the complex barcode by using multiple bc fields. it worked very well.

But when I am trying to process some new scATAC-Seq data with chromap,...... :( the data is pair-end, the barcode mode is : PE1: BC1+Adaptor1+BC2+Adaptor2+my_target_DNA PE2: BC3+Adaptor3+BC4+Adaptor4+my_target_DNA BC1=8bp,BC2=8bp,BC3=8bp,BC4=8bp,Adaptor1=20bp,Adaptor2=20bp,Adaptor3=20bp,Adaptor4=20bp

chromap can process this data? Thanks Tao

[mourisl]

The two-file barcoding system is not supported. You can use the command "paste -d'\0' bc1.fq bc2.fq > pasted.fq" to put the BC1, BC2, BC3 and BC4 into the same line of a new file, and then use the multiple bc option in Chromap. We will think about how to handle the two-file barcoding system in the future.