TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Tophat 2.0.3 is installed on Fourierseq as of 06/11/12.
Very basic Tophat command:
- – bowtie1 can be added to ask tophat to use bowtie1 instead of bowtie2 (bowtie2 does not support colorspace data).
- - C for colorspace (provide csfasta and quality files when using the flag)
Example 1: For mouse:
Example 2: For human:
Cufflinks 2.0.0 is installed on Fourierseq as of 05/24/12
Very basic cufflinks command:
- -G reference.gtf can be added to use reference annotation to assemble transcripts. This will not assemble novel transcripts.
- -g reference.gtf can be added to use the reference annotation as a guide to assemble transcripts. This will include reference transcripts and novel transcripts.
- accepted_hits.bam : bam file created by tophat
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).