I'm just starting to use tophat and I have a little problem which I am not able to solve. I wanna align several human transcriptomes, so I have downloaded the reference human genome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/GRCh38/Homo_sapiens_NCBI_GRCh38.tar.gz) and now I wanna use tuxedo protocol.
Executing the following commands:
1st. Uncompress the genome:
tar xvfz Homo_sapiens_NCBI_GRCh38.tar.gz
2nd. Make a working directory:
3rd. Create symbolic links to annotation files and bowtie index (inside the working directory):
ln -s /path_to/Hsa38/Annotation/Archives/archive-2015-08-11-09-31-31/Genes/genes.gtf ln -s /path_to/Hsa38/Sequence/Bowtie2Index/genome.*.
4th. Try to run tophat (inside the working directory):
tophat -p 8 -G genes.gtf -o sample_output --library-type=fr-firststrand genome sample.fq
The output message was the following one:
[2017-11-07 00:29:47] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2017-11-07 00:29:47] Checking for Bowtie Bowtie version: 22.214.171.124 [2017-11-07 00:29:47] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (genome.*.bt2l)
After that I have tried to finde some file with the extension
find path_to/Hsa38/ -iname *bt2l but I had not success. Does anyone know where is the index? or how can i solve this trouble?
Thanks in advance.