I want to use tophat2 with reference gtf file from UCSC genome browser for which I am supposed to check that the values in the first column of the provided GTF must match the name of the reference sequence in the Bowtie index.
But to check this I tried the Bowtie2-inspect command:
bowtie2-inspect -s hg19index.fa as well as bowtie2-inspect -i hg19index.fa
I get this error:
"Could not locate a Bowtie index corresponding to basename "hg19index.fa""
But the index file worked fine with Bowtie2 as well as tophat2.
Am I making a mistake here, pl clarify,
thanks
But to check this I tried the Bowtie2-inspect command:
bowtie2-inspect -s hg19index.fa as well as bowtie2-inspect -i hg19index.fa
I get this error:
"Could not locate a Bowtie index corresponding to basename "hg19index.fa""
But the index file worked fine with Bowtie2 as well as tophat2.
Am I making a mistake here, pl clarify,
thanks
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