I am pretty new at shell scripting and I have been struggling all day to figure out how to perform a "for" command. Essentially, what I am trying to do is the following:
I have a list.txt file with a bunch of names:
name1
name2
name3
for every name in the list, there are two different files, each with a different ending to the name. Ex:
name1_R1
name1_R2
The program I am trying to run is called sickle
. Basically, it takes two files (that correspond to each other) and runs an analysis on them, hence requiring me to have this naming scheme. The sickle command is as follow:
sickle pe -f input_file1.fastq -r input_file2.fastq -t sanger
If someone could help me out, at least just by telling me how to get unix to read the list of files and treat each line independently I think I could go from there. I tried a few things, but none of them worked.
See Question&Answers more detail:
os 与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…