This seems to be working. Thanks!
I'm trying to run trim galore on multiple files (24), but I haven't gotten it to work. The code I'm using is:
trim_galore /home/name/sequences -j 4 *.fastq.gz -o /home/name --paired
The last message produced is:
Output will be written into the directory: /home/name/
Input file '/home/name/sequences' seems to be completely empty. Consider respecifying!
I know for sure the folder is not empty. All the files are zipped (.fastq.gz). I made a separate folder with unzipped files (.fastq), and it's the same result. I've moved the position of --paired, because I saw somewhere it might work, but it didn't.
I'm running Linux Ubuntu on my Windows computer.
1 answer
I am not a trim galore user but I don't think you can provide trimgalore with a directory name like you did. Based on the usage statement trimgalore is expecting options to follow the program name with input files at the end of the command.
Can you try the following
trim_galore -j 4 -o /home/name/ --paired /home/name/sequences/*.fastq.gz
Log in to answer this question.
What is the output to
file /home/name/sequences?