RNA seq Lib protocol
Submit library to GTAC (log in here to fill out and print the submission form)
Use novoalign to align the sequencing to the custom mRNA list. Here is an updated (2016) version of the database and here is a way to convert from the old list to the new list.
(One time, make an index with the command: novoindex D_rerio.nix Scott_RNA.fa
Then align with something like the command: novoalign -d D_rerio.nix -f <sequence.fastq> > novoaligned.library.txt)
Run this script (perl total_rpkm.pl Scott_RNA.pl novoaligned.library.txt > rpkm.library.txt) to get a tab delimited file that is mrna rpkm.
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