I'm trying to align RNA-seq data of wheat genome so i used bowtie2 with large index option to build the genome index and the results was formated as bt2l instead of bt2 but when i'm running tophat it gives me that error
[2016-04-29 01:29:37] Beginning TopHat run (v2.1.0)
[2016-04-29 01:29:37] Checking for Bowtie Bowtie version: 126.96.36.199 [2016-04-29 01:29:37] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (reference_in.*.bt2)
If i changed the format dose it will work accurately and if not please suggest a solution for that problem.