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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Strandedness - automatic inference #85

Closed uros-sipetic closed 6 years ago

uros-sipetic commented 6 years ago

Hi, currently the user has to specify the '--strandedness' option. However, nowadays it seems that people get FASTQ files and run different analyses with them, without knowing much about them (like the library type, for example). Is it possible to automatically infer the strandedness of input reads, similar to what the Salmon tool already does https://salmon.readthedocs.io/en/latest/salmon.html#what-s-this-libtype ?

bli25wisc commented 6 years ago

@uros-sipetic , sure thing. I'll include this option in future releases. Thanks for the suggestion!

uros-sb commented 4 years ago

Hey @bli25wisc was this ever added to any RSEM release since this issue?