Entering edit mode
19 months ago
mesebaesko
•
0
I am doing transcriptomic analysis and have just started to learn Python. I want my code to read a text file (which has multiple input file names like SRR203456, SRR203457 and so on) and do task of alignment using tool STAR. However, it always give my an error samp.list does not exist. Is there a way to automate it? Help really appreciated. Here is my code
# Execute genome Alignment
genomeDir=/home/RNAseq/
while read samp
do
echo 'STAR --genomeDir '$genomeDir' --readFilesIn '''$samp'''_1.fastq '''$samp'''_2.fastq --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFileNamePrefix '$samp'_ --runThreadN 4' | bsub -M 60000
done < samp.list