Hello everyone,
I am looping my code to run 24 alignments (--very-sensitive-local) for bacterial RNA-Seq.
Here is my code:
for i in ~/Desktop/RNASeq/trimmedreads/*_trimmed.fq.gz;
do "bowtie2 --threads 36 --seed 1234 --fr --very-sensitive-local --no-discordant -t -x ~/Desktop/J53/ -1 $i -2 ${i/_001_trimmed.fq.gz/_002_trimmed.fq.gz}-S "${i%.fq}".sam;
done
There is no output in terminal, only the carrot. Top is a bit non-committal. I am worried it is caught up. I do not see bam directories being created in my current directory (j53). The index ran fine.
Is it just taking forever or did I do something silly? This is my first time looping code.
Of note, I am on a guacamole workstation and not on my local system. I have 36 threads available.
I am looping my code to run 24 alignments (--very-sensitive-local) for bacterial RNA-Seq.
Here is my code:
for i in ~/Desktop/RNASeq/trimmedreads/*_trimmed.fq.gz;
do "bowtie2 --threads 36 --seed 1234 --fr --very-sensitive-local --no-discordant -t -x ~/Desktop/J53/ -1 $i -2 ${i/_001_trimmed.fq.gz/_002_trimmed.fq.gz}-S "${i%.fq}".sam;
done
There is no output in terminal, only the carrot. Top is a bit non-committal. I am worried it is caught up. I do not see bam directories being created in my current directory (j53). The index ran fine.
Is it just taking forever or did I do something silly? This is my first time looping code.
Of note, I am on a guacamole workstation and not on my local system. I have 36 threads available.