I'm trying to use STAR as my aligner, but I get this error:
EXITING because of FATAL ERROR: Read1 and Read2 are not consistent, reached the end of the one before the other one SOLUTION: Check you your input files: they may be corrupted
I checked the logs, and it's my last mate pair, L004, which is causing this issue.
I did a
wc -l on the L004 reads, but they both have the same number of lines. I'm not sure why this error is occurring. Can someone point me in the right direction? This is happening for 8 of my samples. All 8 samples, L004 is behaving the same way.