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ExpressionAnalysis / STAR-SEQR

RNA Fusion Detection and Quantification
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Salmon quant #12

Open jasper1918 opened 7 years ago

jasper1918 commented 7 years ago

As is, starseqr always requires fatqs even if a STAR alignment is provided. If we modify the salmon call to do alignment mode in this scenario we can bypass the fastq requirement

nservant commented 4 years ago

in the same way, salmon -m option is no longer supported

mapostolides commented 4 years ago

Hi there, I am also having trouble with the -m option not working. Is there any way to get around this?

salmon                    1.2.0                hf69c8f4_0    bioconda
salmon quant -i salmon_index -l A -1 ..._1.fq.gz -2 ....fq.gz -o salmon_quant -p 8 -m 400 -w 200 -q
(mapping-based mode) Exception : [unrecognised option '-m'].

UPDATE: I got around this by manually editing the "starseqr_utils/salmon_quant.py" file to exclude the "-m 400" option, but it seems STAR-SEQR is not up to date with this