Hi:
I am not sure if this question has been asked before.
I have 120 RNA-Seq fasta files. I am using tophat2 for aligning to human genome.
I am queing this job on a 70 node cluster. I am using bowtie genome files downloaded from Illumina genome website.
Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome
I see for every fastq file alignment, tophat building index file from genes.fa..
It takes more than 30 minutes for every file.
Can this time consuming process be avoided since we already have index files for bowtie.
Following is my command line:
tophat2 -p 16 \
-G /Refs/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf \
-o tpht \
/Refs/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome \
myfile_1.fastq myfile_2.fastq
Thanks
I am not sure if this question has been asked before.
I have 120 RNA-Seq fasta files. I am using tophat2 for aligning to human genome.
I am queing this job on a 70 node cluster. I am using bowtie genome files downloaded from Illumina genome website.
Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome
I see for every fastq file alignment, tophat building index file from genes.fa..
It takes more than 30 minutes for every file.
Can this time consuming process be avoided since we already have index files for bowtie.
Following is my command line:
tophat2 -p 16 \
-G /Refs/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf \
-o tpht \
/Refs/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome \
myfile_1.fastq myfile_2.fastq
Thanks
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