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Old 05-01-2020, 01:58 AM   #1
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Location: USA

Join Date: May 2020
Posts: 2
Default What is the Bowtie2 default output file extension?

I'm processing samples for atac-seq using this galaxy tutorial ( and I ran this command line:

bowtie2 --dovetail --very-sensitive -X 1000 -k 10 -x /user/mm10/mm10 -1 /user/Cutadapt_res/p4/p4_wt_r1.fastq.gz -2 /user/Cutadapt_res/p4/p4_wt_r2.fastq.gz

I got two output files:

Are these the correct output files I should be getting? Both output files, .e2546134 and .o2546134 doesn't have a extension but the .e2546134 file is openable with a text edit program and shows the alignment info so I assumed the bowtie2 command worked and everything ran and completed.

I want to run the .o2546134 into samtools but before I do that, do I need to manually add in the extension and make it bowtie2_p1.e2546134.bam?

Sorry if this is a common question, it's my first time doing this analysis and I couldn't google the answer.

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