Hi All, how to join multi FASTQ left-hand reads or right-hand reads together? I need map sequence data from different experiments to a common reference, but need first put all left-hand reads or right-hand reads together as one file. Thank you.
If I am getting you right and what you have is a multi-part fastq for the r1 reads of a paired-end run that you want to join together into a single file, and another multi-part fastq for the r2 reads that you also want to join into a single but separate file, then there is the
Concatenate datasets tool for you under Text Manipulation.
Just make sure that you keep the same order of the parts when joining the r1 files and the r2 files so that reads with the same names end up on the same lines in the two files.
If you want to just merge together all left reads into one file and then all right reads into one file, use the tool "Text Manipulation -> Concatenate datasets tail-to-head".
I believe I misunderstood originally and have removed that comment, sorry!
Jen, Galaxy team