Error in aligning bowtie index files with ebwtl format while running tophat

Question

[divchauhan07]

I have used bowtie-1.1.1 to create index files.Now while running tophat

$ /opt/tophat-1.3.0.Linux_x86_64/tophat -o /u01/neeraj1/divya/12hr_fastq/sample/AC12_1/Trim_res/ -r20 /u01/neeraj1/divya/12hr_fastq/sample/AC12_1/Trim_res/1/index /u01/neeraj1/divya/12hr_fastq/sample/AC12_1/Trim_res/paired_R1_1.fastq /u01/neeraj1/divya/12hr_fastq/sample/AC12_1/Trim_res/paired_R2_2.fastq

[Tue Sep 18 13:19:09 2018] Beginning TopHat run (v1.3.0)
-----------------------------------------------
[Tue Sep 18 13:19:09 2018] Preparing output location /u01/neeraj1/divya/12hr_fastq/sample/AC12_1/Trim_res//
[Tue Sep 18 13:19:09 2018] Checking for Bowtie index files
Error: Could not find Bowtie index files /u01/neeraj1/divya/12hr_fastq/sample/AC12_1/Trim_res/1/index.*

my indexing files are in ebwtl format. Both the indexing files and the paired reads are in same folder but m still not able to troubleshoot.

[Bastien Hervé]

* Insert the "don't use TopHat anymore" twitter post here *

[Sej Modha]

Hello divchauhan07,

You should know that the old 'Tuxedo' pipeline of Tophat and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[Bastien Hervé]

Why don't you use bowtie mapping after bowtie indexing ?

[WouterDeCoster]

In addition to the other remarks: please use up to date software. Tophat 1.3.0 was released more than 7 years ago.