Oyster River Strand Exam Tool

The Oyster River Strand Exam Tool, which is adapted from the Trinity Strand Examination script (https://github.com/trinityrnaseq/trinityrnaseq/wiki/Examine-Strand-Specificity) can be used as per the following:

/path/to/Oyster_River_Protocol/strandeval.mk main \
ASSEMBLY=test.fasta \
READ1=1.subsamp_1.cor.fq \
READ2=1.subsamp_2.cor.fq \
RUNOUT=test

This script maps a random 1M reads to the assembly, then plots (plus_strand - minus_strand) / total, which helps us understand the strandedness of the assembly, and if we assembled correctly. Here are the 3 major types of plots you could receive back.

Assembled Correctly

This plot, showing a somewhat normal distribution, is an example of a non-strand-specific library, assembled properly

This plot, showing an extremely biased (can be either left or right side) unimodal distribution, is an example of a strand-specific library, assembled properly. It should be noted that as a result of imperfect library generation (wet-lab issue), there may be a second, smaller peak on the opposite side of the histogram. Basically, the quality of stand-specific libraries varies, and this may introduce noise in this analysis.

Assembled Improperly

This plot, showing an extremely biased bimodal distribution, is an example of a strand-specific library, assembled in a non-strand specific fashion.