I had a multiplexed RNA-Seq run on Hi-Seq machine. The index was part of the Read1, but the Read2 has no index. How can I separate the reads in the Read2 file.
EDIT: I have a Read 1 file R1.fq where the first 6 bases are the barcode. I have R2.fq (the mate file) which has no barcode. I know I can use the fastx barcode splitter to separate the reads from the R1.fq, which I have done. I am not sure how I can now use this R1_sample.fq to fish the specific mate reads from the R2.fq.
I hope this question is now clearer.