Hi there,
We prepared the CRS plasmid library followed your nature protocoland. The library was then subjected to MGISeq 2000 to get the CRS-barcode association (CRS length=220bp, complexity=8Million, PE150) . I run the MPRAflow association.nf followed and found that only very few reads () were kept after join the Read1 and Read2 fastq files (fastq-join -R1 -R2 -o xxx.joint). I am confused about why we need to join the R1 and R2 and then subject to bwa alignment. Is this step critical for the correct assignment of barcode to CRS?
Many thanks,
Clytia
Hi there, We prepared the CRS plasmid library followed your nature protocoland. The library was then subjected to MGISeq 2000 to get the CRS-barcode association (CRS length=220bp, complexity=8Million, PE150) . I run the MPRAflow association.nf followed and found that only very few reads () were kept after join the Read1 and Read2 fastq files (fastq-join -R1 -R2 -o xxx.joint). I am confused about why we need to join the R1 and R2 and then subject to bwa alignment. Is this step critical for the correct assignment of barcode to CRS? Many thanks, Clytia