when trying to map my reads to the index file, it shows an error. please help
$tophat2 genome_index_base reads1.fq reads2.fq
[2022-04-14 12:41:18] Beginning TopHat run (v2.1.1)
[2022-04-14 12:41:18] Checking for Bowtie
Bowtie version: 184.108.40.206
[2022-04-14 12:41:18] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (genome_index_base.*.bt2l)
Did you generate the index for bowtie?
and if so, where are those files located? if they are not in the directory where you are running that cmdline, you will need to add the path to the location where you've placed the index files.
Sorry for the late reply, actually i understood the error , actually the output generated by me through bowtie2 was index not genome_index_base, so that was the error. Command that i wrote for building index was