Tophat transcriptome index

When runnning TopHat with the -G option, it will build a Bowtie index from the provided reference annotation each time. TopHat will output the following lines when doing so:
[..] Building transcriptome data files tophat_out/tmp/genes
[..] Building Bowtie index from genes.fa
Building the index can take quite some time. You can pre-build this index once and use it afterwards each time you run TopHat. To do so, invoke TopHat just with the -G and the --transcriptome-index parameters. TopHat will build an index in the provided location.
$ tophat -G /var/data/bi/reference/prebuild/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf --transcriptome-index /var/data/bi/reference/prebuild/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/transciptome_index/genes /var/data/bi/reference/prebuild/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome
Note that you still have to provide the <bowtie_index> argument. Read the TopHat manual as well. Output:
Building transcriptome files with TopHat v2.1.0
Checking for Bowtie
Bowtie version:
Checking for Bowtie index files (genome)..
Checking for reference FASTA file
Building transcriptome data files /var/data/bi/reference/prebuild/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/transciptome_index/genes
Building Bowtie index from genes.fa
Transcriptome files prepared. This was the only task requested.
Files created:
$ ls -lh /var/data/bi/reference/prebuild/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/transciptome_index/
total 1,7G
-rw-rw-r-- 1 root root 125M Jan  3 17:08 genes.1.bt2
-rw-rw-r-- 1 root root  69M Jan  3 17:08 genes.2.bt2
-rw-rw-r-- 1 root root 1,7M Jan  3 16:56 genes.3.bt2
-rw-rw-r-- 1 root root  69M Jan  3 16:56 genes.4.bt2
-rw-rw-r-- 1 root root 305M Jan  3 16:56 genes.fa
-rw-rw-r-- 1 root root  26M Jan  3 16:56 genes.fa.tlst
-rwxrwxr-x 1 root root 874M Jan  3 16:55 genes.gff
-rw-rw-r-- 1 root root 125M Jan  3 17:19 genes.rev.1.bt2
-rw-rw-r-- 1 root root  69M Jan  3 17:19 genes.rev.2.bt2
-rw-rw-r-- 1 root root   24 Jan  3 16:56 genes.ver
Share itShare on FacebookShare on Google+Tweet about this on TwitterShare on LinkedIn

Leave a Reply

Your email address will not be published. Required fields are marked *