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alexdobin / STAR

RNA-seq aligner
MIT License
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Help for option to output geneBiotype from `geneInfo.tab` to `features.tsv`. #2069

Open galaxy001 opened 7 months ago

galaxy001 commented 7 months ago 
$ head -n6 genome/geneInfo.tab
332285
ENSMUSG00000051951  Xkr4    protein_coding
ENSMUSG00000089699  Gm1992  lncRNA
ENSMUSG00000102331  Gm19938 lncRNA
ENSMUSG00000102343  Gm37381 lncRNA
ENSMUSG00000025900  Rp1 protein_coding

$ head -n6 features.tsv
ENSMUSG00000051951  Xkr4    Gene Expression
ENSMUSG00000089699  Gm1992  Gene Expression
ENSMUSG00000102331  Gm19938 Gene Expression
ENSMUSG00000102343  Gm37381 Gene Expression
ENSMUSG00000025900  Rp1 Gene Expression
ENSMUSG00000025902  Sox17   Gene Expression

soloOutFormatFeaturesGeneField3 can only set field3 to a fixed string, it is helpful to copy the original biotype. Would you make --soloOutFormatFeaturesGeneField3 COPY or sth. like this ?