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For various reasons, at some point, you will want to map your RNAseq data onto your assembled genome.
Unless you have a prokaryotic genome or a eukaryotic genome with intronless genes you need a mapper that can properly deal with spliced alignments. Tophat2 is widely used and cited https://ccb.jhu.edu/software/tophat/index.shtml but has now been superseded by HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml
Before you can map your RNAseq reads to your genome you need to build an index of the genome assembly.
In a shell script that you can qsub include the following line
/scratch2/software/hisat2-2.1.0/hisat2-build -f name_of_genome_assembly.fasta root_for_index
This will create a series (depending on the size of the genome) of files with the root name eg
pce_p3x.1.ht2
pce_p3x.2.ht2
pce_p3x.3.ht2
Once the indices have been built you can proceed with the actual mapping. There are many options available http://ccb.jhu.edu/software/hisat2/manual.shtml but for our purposes we will restrict them to the bare essentials.
A typical shell script to qsub would look like this #!/bin/sh #$ -o logo_p3x_hisat #$ -cwd #$ -pe threaded 6
/scratch2/software/hisat2-2.1.0/hisat2 -q -p 6 –phred33 –max-intronlen 1000 -k 2 -x pce_p3x -1 PCE_RNA_1_PairNtrim.fastq -2 PCE_RNA_2_PairNtrim.fastq -S pce_3x.sam