I am fairly new to RNA-seq. I am trying to use Tophat for RNA-seq read alignment, and am trying to save the Bowtie index built as part of the alignment process. According to the Tophat Manual the way to do this is to use the
-G flag, followed by the
--transcriptome-index flag. To that end I have written a shell script that makes use of this feature (relevant portion below):
ebwt=/home/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome gtf=/home/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf refFastq=/home/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa known=/home/Homo_sapiens/UCSC/hg19/Annotation/Genes/known output="tophat_20120917" dir="/home/"$lane"/" cd $dir tophat -G $gtf --transcriptome-index=/home/known --solexa1.3-quals -o $output --library-type fr-unstranded $ebwt $left 1>stdout.txt 2>stderr.txt
However, when I run the script, I get the following output to
[2012-09-26 11:16:48] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/home/known.*.bt2)
What am I doing wrong? It seems like the
--transcriptome-index flag is overriding the
-G flag, but this shouldn't be happening.
Any advice is appreciated!