Hi all,
Ultimately aiming at differential expression, I'm mapping human RNAseq read using tophat2 with the following command:
Is it really necessary to:
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
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
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
Cheers,
Leon
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