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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 Tophat2 is widely used and cited  https://ccb.jhu.edu/software/tophat/index.shtml but has now been superseded by HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml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
<code>
#!/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
</code>

where

-q indicates that the reads are in fastq format versus -f for fasta

-p 6 indicates how many threads to use

--phred33 indicates that scoring scheme for the quality scores

--max-intronlen 1000 indicates that you believe that the longest real intron is 1000 bps (default is 50,000)

-k 2 indicates how many distinct primary alignments to search for for each read

-x pce_p3x is the index root name

-1 PCE_RNA_1_PairNtrim.fastq indicates the file for the forward (/1) reads

-2 PCE_RNA_2_PairNtrim.fastq indicates the file for the reverse (/2) reads

-S pce_3x.sam indicates the name for the SAM output file

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