Thank you for the timely response. I ran the echo command and my output is below:
STAR --genomeDir Star_index/Mcal_index --runMode alignReads --runThreadN 10 --readFilesIn /home/terceroa/Projects/M.cal/Data/Tagseq/Trim/Cat_trim/Star_subset/ATMCG001.trim.fa.gz /home/terceroa/Projects/M.cal/Data/Tagseq/Trim/Cat_trim/Star_subset/ATMCG002.trim.fa.gz /home/terceroa/Projects/M.cal/Data/Tagseq/Trim/Cat_trim/Star_subset/ATMCG003.trim.fa.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFileNamePrefix *.fa.gz
I agree that the $i variable contains more than one file as it is grabbing all three files in my test directory. I am confused about where to press on from here. I was under the assumption that the loop would see all files in my test directory (indicated by the *.fa.gz) command, then iterate through the list and create an output for every filename. Do you have any advice for constructing my for-loop?
Thank you for your time, it is greatly appreciated