bowtie2: aligning multiple input files

[ksw9]

Hi all,

I am new to using Bowtie2 and am having trouble aligning multiple input files. I have 24 sets of input sequence reads for each pair (24 files for mate 1 and 24 files for mate 2) which I hope to align to a reference genome.

bowtie2 -x index -1 file1_*.fastq -2 file2_*.fastq -S output.sam


I keep getting error messages: Warning: Output file was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Extra parameter(s) specified...
Note that if <mates> files are specified using -1/-2, a <singles> file cannot
also be specified. Please run bowtie separately for mates and singles.

I think there is some issue in specifying multiple input files for each mate pair using the * to denote all the files which correspond to reads for each matepair. Is there something obvious I can change?

Thank you!

[dpryan]

Yes, the manual states that you must separate multiple files by a comma, which you're not doing. Have a look at this comment. It relates to STAR, but the principle is the same.

[ksw9]

Okay that makes sense, thanks for your help!