SHRiMP - Which parameters for aligning to miRNAs?

[all_your_base]

Hi,

I recently read a few reviews that point to SHRiMP as the short read aligner of choice when mapping small RNA-seq reads to a database of miRNAs.

SHRiMP even includes a miRNA parameter, but is very vague as to what the parameters do and how to optimize. I've emailed the dev team but never received a response.

I'll show everyone what I tried for my first attempt mapping these small RNA-seq reads to a miRNA database, and please offer suggestions for optimization or correct any errors in my command.


I first projected the database:
SHRiMP-2.2.3/utils/project-db.py --seed 00111111001111111100,00111111110011111100,00111111111100111100,00111111111111001100,00111111111111110000 --h-flag --shrimp-mode ls refs/all_mature_miRNAs.fa

I then mapped to the database:
SHRiMP-2.2.3/bin/gmapper-ls -L all_mature_miRNAs-ls --fastq --qv-offset 33 my_reads.fastq --mode mirna >map.out

According to the SHRiMP documentation, passing the --mode mirna parameter does the equivalent of entering the following:
"loading the 5 seeds mentioned above; plus '-H -n 1 -w 100% -U -a 0 -g -255 -q -255 -Z'"


If you have any experience using SHRiMP for this purpose, I'm eager to hear your advice. Thanks!

[Giorgio C]

Hi, I know it's an old post but I was wondering if you finally get the right way, in terms of parameter, for the analysis of miRNA in Shrimp.

Since I have to start from the beginning and there is not so much documentation out there, I want to be sure of what I'm going to do.

Hope to have some advices from you.

Thanks in advance,
Giorgio