Could not locate a Bowtie index corresponding to basename "mm9"
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
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Maybe you can check the directory path of mm9 index files (such as mm9.1.bt2, mm9.2.bt2 ....).
Hello, yaochung41, Thank you for your response!
This works!
bowtie-build mm9.fa mm9.fa
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
Hello, cpad0112, Thank you for your response!
This works!
bowtie-build mm9.fa mm9.fa
Please show output of
lswhile being in that folder. Also, no need to do that unzipping,bowtiewill happily accept compressed files.Hello, ATpoint, Thank you for your response!
This works!
bowtie-build mm9.fa mm9.fa
Good to hear, still no need to make the same post under each comment.