bowtie2, and python script
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16 months ago
qudrat.nii ▴ 10

Hello, I am trying to do bowtie2 alignment for 100 fastq files. To run bowtie2 alignment I am trying to write a python script but I am stuck at writing ''for loop''. Please help me. Thank you

and python bowtie2 script • 1.5k views
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A simple bash script would probably serve you better, or a Makefile. Alternatively a workflow manager such as Snakemake which is python-ish. Please show what you tried.

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import subprocess folder = "/Desktop/RNA-Seq" fastq_file = [] try: for files in folder: if files.endswith('fastq'): fastq_files.append(files) subprocess.run("bowtie2 -x folder/bt2_idx -1 f1.q -2 f2.q -S f.sam") except: print('some error')

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What is error you're getting here? What are the f1.q and f2.q. Also, please format your code blocks.

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f1.q and f2.q is fastq file. Actually I am not able to write the script which can take pairs of files as input for bowtie2

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Here is a snippet that can help you do that:

https://stackoverflow.com/questions/312443/how-do-i-split-a-list-into-equally-sized-chunks

However, you should listen to other's advices here and look into shell or workflow managers.

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