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Old 04-01-2018, 08:27 AM   #1
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Location: Israel

Join Date: Apr 2018
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Default Alignment with bowtie doesn't creates .sam file


I'm trying to align a fastq.gz file with bowtie.
My script is:
${bowtie_source} --sam --best ${ref_genome} ${fastq_file}

But it doesn't carets a new .sam file.
How to fix the script in order to get a .sam file in a desired directory?
Pery is offline   Reply With Quote
Old 04-02-2018, 08:45 PM   #2
Location: MA, USA

Join Date: Feb 2014
Posts: 58

I think you need to specify the output file. For example, add "-S new_file.sam" to the script.


neavemj is offline   Reply With Quote

bowtie, sam

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