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  • Bowtie2 Question

    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.
    ​
    Last edited by Faya; 05-13-2024, 07:39 AM.

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