Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

producing strandedness metrics from rnaseq data


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    Pamela Bretscher

    Hi AMN,

    I don't believe there is a way to get strandedness metrics if you use STRAND=NONE as you are specifying to CollectRnaseqMetrics that there is no strandedness. You could try to use 'FIRST_READ_TRANSCRIPTION_STRAND' to get the metrics you are looking for but I don't know how accurate or useful this would be for unstranded data. 



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