Hello All!
I am new to coding and am trying to write a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess module to call bowtie2 in order to index the genome that is in fasta format. That works just fine. But I am stuck in the next step which is using bowtie2 to align the unpaired short reads to the genome. I know I am using the correct command as it works at the terminal generating a .sam file. But my python code is not working. Here are some of the ones I have tried--
#process = subprocess.call (['bowtie2_align', indexfiles, fastqFile1, Outputfile])
#process = subprocess.Popen(['bowtie2_align', stdin= indexfile, fastqFile1, stdout=Outputfile])
#process2 = subprocess.call(["bowtie2_align" (-x indexfile, -U fastqFile1, -S 'Outputfile.sam')],shell=True)
align = 'bowtie2_align' -x cellvibrio_index -U fastqFile1 -S initial_aligns.sam'
I would really appreciate any help/suggestions to fix this code.
Thanks,
-M
I am new to coding and am trying to write a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess module to call bowtie2 in order to index the genome that is in fasta format. That works just fine. But I am stuck in the next step which is using bowtie2 to align the unpaired short reads to the genome. I know I am using the correct command as it works at the terminal generating a .sam file. But my python code is not working. Here are some of the ones I have tried--
#process = subprocess.call (['bowtie2_align', indexfiles, fastqFile1, Outputfile])
#process = subprocess.Popen(['bowtie2_align', stdin= indexfile, fastqFile1, stdout=Outputfile])
#process2 = subprocess.call(["bowtie2_align" (-x indexfile, -U fastqFile1, -S 'Outputfile.sam')],shell=True)
align = 'bowtie2_align' -x cellvibrio_index -U fastqFile1 -S initial_aligns.sam'
I would really appreciate any help/suggestions to fix this code.
Thanks,
-M
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