Error: Could not find Bowtie 2 index files (splice-mismatch.*.bt2)

Question

[ALI Hkz]

hi i am running tophat2 and bowtie2 , these are my commands and i couldn't get the result:

tophat2 -p 16 --keep-fasta-order -o ./tophat_out_${NAME}\
 --read-mismatches 4\
 --read-gap-length 4\
 --read-edit-dist 4\
 --read-realign-edit-dist 0\
 --min-anchor 4\
 -- splice-mismatch 1\
 --GTF gencode.v19.annotation.gtf\
 --transcriptome-index= transcriptome/\
 genome/Homo_sapiens.bowtie_index\
 trimmed_cut1SRR5481725.fastq trimmed_cut2SRR5481725.fastq

and that's the error massage that i face:

[2018-12-05 09:23:33] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (splice-mismatch.*.bt2)

[Bastien Hervé]

Please do not use Tophat anymore, the author himself said it's outdated

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

HISAT2 and STAR are both splice aware solution

[WouterDeCoster]

Hmmm the command you show doesn't match with the error you get?

Answer 1

[Devon Ryan]

You have a space in -- splice-mismatch. As mentioned in the comment, you should not be using tophat for anything.