parameter

[WeiXu63]

What's the default parameter for flanking sequence in mirdeep2? How can I adjust it? Thanks.

[Drmirdeep]

Based on your unclear question the answer is 42.

[WeiXu63]

Hello Drmirdeep,

Sorry for the unclear question. I want to use mirdeep2 to analyze my plant small RNAseq data. According to the literatures I found, I learned the default parameters of mirdeep2 is good for animal small RNAseq data; for plant small RNAseq data, I need to adjust some parameters, i.e. some authors, adjusted the sRNA<=15 hits, and 250nt flanking sequences (on each side on the genome) for plant miRNA analysis. Let's me just quote the original sentence from their manuscript "miRNA Identification. The unannotated reads containing miRNAs were processed for miRNA identification by miRDeep2 v 2.0.0.531 with modified parameters (sRNAs ≤ 15 hits; 250 nt flanking sequences) for plant miRNA characters30. In brief, the analysis procedure of miRDeep2 were: (1) The unannotated reads were aligned to the Jatropha genome sequences using Bowtie v 0.12.9 with perfect matches, and only sRNAs with no more than 15 hits were kept and their flanking sequences (250 nt on each side) on the genome were extracted as candidate miRNA precursors, to satisfy the parameters of miRNAs in plant species as described."

When I use mirdeep2 to analyze my data, I used mapper.pl to align my samples reads to the genome, but I found -r parameter can be used to adjust the hits, but I didn't find a parameter to adjust the flanking sequences. Could you let me know which parameter it is? This is my question. Thanks. Xu

[mschilli87]

duplicate of https://github.com/rajewsky-lab/mirdeep2/issues/83