Tophat running error

Question

[mahnazkiani]

Hello,

I'm trying to run tophat and I'm getting the following error that I don't know how to fix it. Appreciate any help.

[2018-05-11 11:14:58] Checking for Bowtie
                  Bowtie version:        2.2.9.0
[2018-05-11 11:14:58] Checking for Bowtie index files (genome)..
[2018-05-11 11:14:58] Checking for reference FASTA file
[2018-05-11 11:14:58] Generating SAM header for ./Stuberosum_448_v4.03
[2018-05-11 11:14:59] Reading known junctions from GTF file
[2018-05-11 11:15:02] Preparing reads
         left reads: min. length=150, max. length=150, 34720645 kept reads (20 discarded)
        right reads: min. length=150, max. length=150, 34720291 kept reads (374 discarded)
[2018-05-11 11:38:41] Building transcriptome data files ./Top_13/tmp/Stuberosum_448_v4.03_gene_exons
[2018-05-11 11:38:55] Building Bowtie index from Stuberosum_448_v4.03_gene_exons.fa
[2018-05-11 11:40:44] Mapping left_kept_reads to transcriptome Stuberosum_448_v4.03_gene_exons with Bowtie2
Error locating program: fix_map_ordering

Answer 1

[GenoMax]

This means the directory where your tophat program executables are present is not in your $PATH.

You can fix this by doing export PATH=$PATH:/name_of_directory_with_tophat_executables and re-run.

[Deepshikha]

It solved the problem for me.