Genome Guided Trinity Transcriptome Assembly
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Genome-guided Trinity De novo Transcriptome Assembly
If a genome sequence is available, Trinity offers a method whereby reads are first aligned to the genome, partitioned according to locus, followed by de novo transcriptome assembly at each locus. In this use-case, the genome is only being used as a substrate for grouping overlapping reads into clusters that will then be separately fed into Trinity for de novo transcriptome assembly. This is very much unlike typical genome-guided approaches (eg. cufflinks) where aligned reads are stitched into transcript structures and where transcript sequences are reconstructed based on the reference genome sequence. Here, transcripts are reconstructed based on the actual read sequences.
Why do this? You may have a reference genome, but your sample likely comes from an organism with a genome that isn't an exact match to the reference genome. Genome-guided de novo assembly should capture the sequence variations contained in your RNA-Seq sample in the form of the transcripts that are de novo reconstructed. In comparison to genome-free de novo assembly, it can also help in cases where you have paralogs or other genes with shared sequences, since the genome is used to partition the reads according to locus prior to doing any de novo assembly. If you have a highly fragmented draft genome, then you are likely better off performing a genome-free de novo transcriptome assembly.
Users must provide read alignments to Trinity as a coordinate-sorted bam file. Use GSNAP, TopHat, STAR or other favorite RNA-Seq read alignment tool to generate the bam file, and be sure it's coordinate sorted by running 'samtools sort' on it.
To run Genome-guided Trinity and have Trinity execute GSNAP to align the reads, run Trinity like so:
Trinity --genome_guided_bam rnaseq.coordSorted.bam \ --genome_guided_max_intron 10000 \ --max_memory 10G --CPU 10
Of course, use a maximum intron length that makes most sense given your targeted organism.
Be sure to include additional options such as '--SS_lib_type' and '--jaccard_clip' where appropriate. If quality trimming or normalization are desired, these processes should be performed prior to aligning the reads to the genome, as Trinity will only use the reads as they exist in the coordinate-sorted bam file provided to it.
If you specify --grid_conf , then the commands in this second phase will be executed in parallel on your compute farm, using LSF, SGE, or other supported method. Otherwise, these commands will be executed locally using our Parafly parallel command processor, throttled at --CPU number of parallel processes.