Error: Could not find Bowtie 2 index files (/scratch/Genomes/Ptrichocarpa/assembly/Ptr_210_3.*.bt2l)

Question

[jmac.macrae]

tophat2  -o myallignments --transcriptome-index=/scratch/Genomes/Ptrichocarpa/assembly/Ptr_210_3.tr/Ptr_210_3  -p 18 -i 15 -I 15000 -r 50  /scratch/Genomes/Ptrichocarpa/assembly/Ptr_210_3 Sample180_fwd_paired.fq Sample192_rev_paired.fq

I have the following code, I am not sure if there is an error in the way i have written out the path to the indexed files? I am using tophat and bowtie.

[h.mon]

Tophat authors are saying it shouldn't be used any longer, for quite some time now:

https://ccb.jhu.edu/software/tophat/index.shtml

Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.

Or:

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

[afli]

Hi, do you use the following command:

bowtie2-build genome.fa genome
bowtie2 -x genome -1 file1.fastq -2 file2.fastq -S file.sam

Answer 1

[chipeyown]

Please make sure that there are just Bowtie2 indexes in the index directory. If you build Bowtie1 and Bowtie2 indexes in the same directory, this problem will arise.(see the check_bowtie_index function in tophat).Maybe you can also solve this problem by replace (idxext="bt2l") with (idxext="bt2") in tophat.