error in tophat2

Question

[zizigolu]

hi,

I have already built index for genome fasta by bowtie2-build genome.fa aspergillus.fumigatus

but I don't know why tophat can't find them :(

[izadi@lbox200 bowtie2-2.2.9]$ $TOP/tophat -p 8 -G Aspergillus_fumigatus.CADRE.32.gtf -o 1_thout genome.fa clean.fq

[2016-09-03 01:01:10] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2016-09-03 01:01:10] Checking for Bowtie

          Bowtie version:    2.2.9.0

[2016-09-03 01:01:10] Checking for Bowtie index files (genome)..

Error: Could not find Bowtie 2 index files (genome.fa.*.bt2l)

[izadi@lbox200 bowtie2-2.2.9]$

helpless...

Answer 1

[Satyajeet Khare]

Build genome

bowtie2-build -f genome_bowtie2_build/genome.fa genome_bowtie2_build/genome

That is, keep the name of build files same as that of fasta file and preferably keep them in the same location.

Run tophat. genome_bowtie2_build/genome is the location of genome build files (try removing .fa from your command).

tophat2 -p 10 -o tophat2/sample1/ genome_bowtie2_build/genome sample1.fastq

If you want to provide gtf file, build transcriptome. Genome build location is also provided in the command.

tophat -G basic.annotation.gtf --transcriptome-index=./transcriptome_data/basic.annotation genome_bowtie2_build/genome

and then run tophat with gtf file

tophat2 -p 10 -G basic.annotation.gtf --transcriptome-index transcriptome_data/basic.annotation -o tophat2/Sample1 genome_bowtie2_build/genome sample1.fastq

But if you starting, may be you should start with Hisat.

[zizigolu]

thank uuuuuuuuuuuuuuuuuuuuuuuuuuuu extend to the world u saved me from confusion

[k.kathirvel93]

Hi Satyajeet, From where I can get the basic.annotation.gtf file. Thanks in advance for your help.