Discussions about BRAKER, the automated joint usage of GeneMark and AUGUSTUS.
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I have a large paired-end RNAseq library for my organism, prepared with a stranded protocol . I have a single BAM file that was created by mapping those reads to my organism's new genome (using BWA mem).
The BRAKER manual says BRAKER can exploit RNAseq library strandedness
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...for UTR training and prediction, stranded libraries may provide information that is valuable for BRAKER.
After alignment of the stranded RNA-Seq libraries, separate the resulting bam file entries into two files: one for plus strand mappings, one for minus strand mappings.
Can you explain what this means in practice? Conceptually, for paired end reads, I interpret a 'plus strand mapping' as being where the Forward read of a read pair maps to the plus strand (so its Reverse read maps to the minus strand). A minus strand mapping would be where the Forward read maps to the minus strand of the reference (so its Reverse read maps to plus strand.)
Is this correct and is there a common way to split a conventional bam file to generate the required two files?