have trouble with bowtie2

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7.5 years ago

mikysyc2016 ▴ 120

what i can do? Thanks

~$ bowtie2 -x '/home/yachen/Desktop/wu_0.v7.fas'  '/home/yachen/Desktop/wu_0_A_wgs.fastq' -S wu_0.bt2.sam
(ERR): "/home/yachen/Desktop/wu_0.v7.fas" does not exist or is not a Bowtie 2 index
Exiting now ...

RNA-Seq ChIP-Seq • 2.1k views

ADD COMMENT • link 7.5 years ago by mikysyc2016 ▴ 120

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-x option needs to point to the basename of several files that form the set of index files. What command did you use to create the bowtie2 index?

If you have not created the bowtie2 index then you need to do that first using bowtie2-build command.

ADD REPLY • link 7.5 years ago by GenoMax 154k

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I have bowtie2 index. Still thank you for your reply!

ADD REPLY • link 7.5 years ago by mikysyc2016 ▴ 120

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What is the filename of your bowtie2 index?

ADD REPLY • link 7.5 years ago by d-cameron ★ 3.0k

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please post ls *.bt2* output (if you are on os X or linux)

ADD REPLY • link 7.5 years ago by cpad0112 21k

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