Could not locate a Bowtie index corresponding to basename "mm9"

Question

[yueli7]

Hello, I got this message.

Thanks for any help!

Best,

Yue

lixxx:~/umi_tools_example$ bowtie --threads 4 -v 2 -m 10 -a mm9 <( gunzip < processed.fastq.gz ) --sam > mapped.sam
Could not locate a Bowtie index corresponding to basename "mm9"
Command: /usr/bin/bowtie-align-s --wrapper basic-0 --threads 4 -v 2 -m 10 -a --sam mm9 /dev/fd/63

[yaochung41]

Maybe you can check the directory path of mm9 index files (such as mm9.1.bt2, mm9.2.bt2 ....).

[yueli7]

Hello, yaochung41, Thank you for your response!

This works!

bowtie-build mm9.fa mm9.fa

[cpad0112]

Did you index the reference genome ? If so, you might have given base name for indexing. That base should be provided here instead of mm9. @ yueli7

[yueli7]

Hello, cpad0112, Thank you for your response!

This works!

bowtie-build mm9.fa mm9.fa

[ATpoint]

Please show output of ls while being in that folder. Also, no need to do that unzipping, bowtie will happily accept compressed files.

[yueli7]

Hello, ATpoint, Thank you for your response!

This works!

bowtie-build mm9.fa mm9.fa

[ATpoint]

Good to hear, still no need to make the same post under each comment.