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Very basic Tophat command:
| Code Block |
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nohup tophat \-p 4 \-r <mate-inner-distance> \-G <gfffile> <bowtie_index_prefix> <R1.fasta> <R2.fasta> &>tophat.log & |
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Example 1: For mouse:
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nohup tophat \-p 4 \-r 130 \-G /usr/local/genome/references/mmu_ncbi37/mm9_ucsc-known.gff3 /usr/local/genome/references/mmu_ncbi37/mmu_masked_ncbi37.fasta sim.test1.forward.fa sim.test1.reverse.fa &>tophat.log & |
Example 2: For human:
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tophat \--transcriptome-index=/usr/local/genome/references/hg19/bowtie_gtf_index/hg19.gtf /usr/local/genome/references/hg19/bowtie_index/hg19.bs.bowtie <reads.fq>
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An error during the segment mapping step with tophat 2.0.2 (Error: segment-based junction search failed with err =1) has been encountered that is solved by not using multiple threads (-p option).\