I'm trying to infer the the type of experiment for my paired-end RNAseq data.
I have employed STAR to index the genome and map the paired reads (as unstranded) to derive the experiment. Depending on the bed file I employ to infer the experiment I get different results.
As genome I'm employing the genecode: 

> GRCm39.primary_assembly.genome.fa

Anyone can guess why are these differences happening?


**Method 1 (bed converted from genecode gtf)**


Convert gtf to bed

    bedparse gtf2bed gencode.vM27.annotation.gtf > gencode.vM27.annotation.gtf.bed

**Code**

    infer_experiment.py -r /local/ref/gencode.vM27.annotation.gtf.bed -i /local/out/star/ADU2124Aligned.sortedByCoord.out.bam

**Result:**

    This is PairEnd Data
    Fraction of reads failed to determine: 0.1017
    Fraction of reads explained by "1++,1--,2+-,2-+": 0.0080
    Fraction of reads explained by "1+-,1-+,2++,2--": 0.8903

**Method (bed file provided by rseqc)**

**Code**

    infer_experiment.py -r /local/ref/mm10_Gencode_VM18.bed -i /local/out/star/ADU2124Aligned.sortedByCoord.out.bam

**Result**:

    This is PairEnd Data
    Fraction of reads failed to determine: 0.0577
    Fraction of reads explained by "1++,1--,2+-,2-+": 0.3863
    Fraction of reads explained by "1+-,1-+,2++,2--": 0.5560



Thanks!

Well, it seems that I was employing the wrong bed from rseqc and I didn't notice until now...

> **BED:** mm10_Gencode_VM18.bed 
>
> **Reference:** GRCm39.primary_assembly.genome.fa