Question: error in tophat2
gravatar for A
4.1 years ago by
A3.9k wrote:


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:

[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]$


rna-seq software error • 1.5k views
ADD COMMENTlink modified 4.1 years ago by geek_y11k • written 4.1 years ago by A3.9k
gravatar for Satyajeet Khare
4.1 years ago by
Satyajeet Khare1.6k
Pune, India
Satyajeet Khare1.6k wrote:

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.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Satyajeet Khare1.6k

thank uuuuuuuuuuuuuuuuuuuuuuuuuuuu extend to the world u saved me from confusion

ADD REPLYlink written 4.1 years ago by A3.9k

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

ADD REPLYlink written 3.0 years ago by k.kathirvel93260
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