From reading around, I'm not sure whether a solution has been found to the problem of the FASTq joiner tool.
I am trying to combine left and right reads from RNA-seq data into one file, before cutting my adapter sequences and aligning with Tophat.
As I had data across two lanes for 1 sample, i first concatenated files from both lanes for left and right reads respectively. I have then tried to join the concatenated datasets. My data is in the newer format.
Can anybody offer a solution to this problem?
Thank you for your help.