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

alignment
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updated by chipeyown • chipeyown • written by jmac.macrae • jmac.macrae

Hi, do you use the following command:

bowtie2-build genome.fa genome
bowtie2 -x genome -1 file1.fastq -2 file2.fastq -S file.sam
• 1 views • link
written by afli afli

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Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.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

• 1 views • link
written by h.mon h.mon

1 answer

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.

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written by chipeyown • chipeyown

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