A fast aligner for short reads. This is comparable to bwa but previous versions were shown to be less sensitive.
Requires genome file to be indexed just like bwa does.
$ bowtie-build genome.fa genome # or (better to try and use bowtie2 which is faster) $ bowtie2-build genome.fa genome
Basis for the alignments used in TopHat which supports spliced alignment.
$ tophat genome -G genome_annotation.gtf rnaseq_1.fq rnaseq_2.fq
How to align when the short reads may be interrupted by introns in the genome? Spliced alignment can be made aware of potential sites
For comparing expression values. This will generate table of expression values per transcript and gene unit.
$ cufflinks -G genome.gff -I MAX_INTRON_SIZE --library-type [fr-unstranded] tophat/accepted_hits.bam
Cufflinks will generate transcript models de-novo from annotation.
$ module load trinity-rnaseq $ ulimit -s unlimited $ Trinity.pl --max_memory 30G --CPU 20 --kmer_method inchworm \ --seqType fq --left Neo_RNA_seq-RNA_l1_1.fq \ --right Neo_RNA_seq-RNA_l1_2.fq --output trinity_out \ --jaccard_clip