bam_to_junc_bed.py was intended to require a minimum number of reads before reporting a junction. @pRottinghuis made a pull request to the intronProspector repo requesting this feature; it has been merged.
To do: recreate the u2af1 genotype signature/recall example including a read count threshold at the intron prospector step. The example shows that using the intron prospector implementation generates the same results as what we previously saw with bam_to_junc_bed.py in splicedice. Specifically, building a signature based on the u2af1 genotype (35 wt, 11 s34f) creates a signature that then correctly re-identifies each of the samples used to generate it.
bam_to_junc_bed.py was intended to require a minimum number of reads before reporting a junction. @pRottinghuis made a pull request to the intronProspector repo requesting this feature; it has been merged.
To do: recreate the u2af1 genotype signature/recall example including a read count threshold at the intron prospector step. The example shows that using the intron prospector implementation generates the same results as what we previously saw with bam_to_junc_bed.py in splicedice. Specifically, building a signature based on the u2af1 genotype (35 wt, 11 s34f) creates a signature that then correctly re-identifies each of the samples used to generate it.