Which one of these sRNA prediction tools is better?

Question

[jomagrax]

Hi everyone!

Im trying to analyce a small RNA-seq, for the sRNA identification of bacteria I've found a lot of tools, so many in fact that I'm a little overwhelm, these are the ones I've found;

APERO, DETR’PROK, sRNA-Detect, TLA from RNA-eXpress, Rockhopper, ANNOgesic and the two in-house GL and Nuss

Can anyone recommend any of the above or a different one?

Thanks in advance, Jose.

Answer 1

[wm]

I would give my vote to APERO. The reason is I agree with the idea detecting the both boundaries for sRNA prediction. (I did not compare above methods, anyway, APERO paper did it).

However, we should be very careful for the full length for any method.

Answer 2

[jomagrax]

I have heavily considered using APERO but I don´t know If It can be used with single-end data as mine.

[wm]

The APERO algorithm support paired-end reads only, according to their paper. I tried to cut both ends of the SE reads, and save as PE reads (reverse-complement the 3' end of SE reads as "read2"). I did this way years ago when I tried to "detect" sRNAs. (75SE, 101SE).

[cervantesriveraramon]

I'm trying to run APERO like this:

library(Rsamtools) library(reshape2) library(snowfall)

library(APERO)

Load annotation file

ptt=read.csv("/Users/ramon/Desktop/SmallRNA/NZ_CP037923_24.ptt",sep="\t",skip=2,header=T,stringsAsFactors = F)

5'end detection

res=APERO_start_detection(work_dir = "/Users/ramon/Desktop/SmallRNA/", bam_name = "Intra.bam", ptt_file =ptt , wmax = 10, min_dist = 10, enrichment = 0.1, min_read_number = 0, genome_size = 4828909)

It did not work. I have not gotten any output.

Can some one help me??