What I'm trying to do is really straightforward - align ribosome profiling reads (only mRNA fragments protected from RNase degradation are sequenced) to the mouse transcriptome. I've completed this using the following:
I first ran my fastq file through FastQC. I noticed there was a lot of adapter contamination, so I ran my fastq through cutadapt/trim_galore. The output file appeared free of illumina adapters.
I then aligned to the transcriptome using Hisat2 w/ genome/transcriptome I downloaded from their website (GRCm38 genome_snp_tran files [I think this is what I want in order to align to the transcriptome?]). My command was as follows:
hisat2 -x [genome/transcriptome index] -U [single end read file].fastq -S [output file name].sam
samtools for SAM to sorted BAM conversion
Gene abundance using Cufflinks w/ command:
cufflinks -G [transcriptome annotation].gtf [input sorted bam]
Ultimately, the results looks okay. I did get a lot of unmapped reads (~30%) from Hisat2 alignment. This may have to do with the fact that the mice I'm using are not C57Bl6. Don't know if hisat2 genome/transcriptome build I'm using accounted for all snps.