I have pair-end files, what is the normal step to proceed remove the adapters and barcode seq or the other way around? I probably will use FASTX toolkit if it is suitable?
@HWI-ST1075L:227:S1FDTG6ACXX:8:1101:1329:2093 1:N:0:ACAGTG AAGCCGATCAGATACCTGGAATTCTCGGGTGCCAAGGAANTNNAGNNACNCAGTGANCTCNTATGCCGTNTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAA ++
Is the analysis should be done in file pairs R1 R2 or?
Its strange to see 100bp PE data for miRNA. You should definitely remove the adapters then.
and the Barcode probably after that?
The strange question is after I clean the R1 and R2 what to do if it is pair-end if it is miRNA? what is actually the data on the R2?!
Do you have a dual indexed sample? If so, I would go for fastx' barcode splitter.
Otherwise, you'll find the barcode in the read-name:
What you highlight is rather the illumina index than the barcode right ?