SHRiMP - Which parameters for aligning to miRNAs?

all_your_base · 10-18-2012, 02:07 PM

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 · 03-14-2013, 05:21 PM

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

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10-18-2012, 02:07 PM	#1
all_your_base Member Location: USA Join Date: Mar 2012 Posts: 40	SHRiMP - Which parameters for aligning to miRNAs? 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!

03-14-2013, 05:21 PM	#2
Giorgio C Member Location: ITALY Join Date: Oct 2010 Posts: 89	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