View Single Post
Old 09-18-2014, 01:20 AM   #1
LeonDK
Member
 
Location: Denmark

Join Date: Sep 2014
Posts: 69
Default TopHat2 on multiple samples, avoid building Bowtie index from genes.fa each time?

Hi all,

Ultimately aiming at differential expression, I'm mapping human RNAseq read using tophat2 with the following command:
Code:
tophat2 --num-threads 12 --GTF /Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf /Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome myfastq_R1.fastq.gz myfastq_R2.fastq.gz
Is it really necessary to:
Code:
[2014-09-18 10:38:45] Building transcriptome data files /tmp/genes
[2014-09-18 10:39:21] Building Bowtie index from genes.fa
Foreach sample? I mean - The different samples are all mapped using the same Bowtie2Index/genome files and the same Genes/genes.gtf files?

Cheers,
Leon
LeonDK is offline   Reply With Quote