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wenweixiong / MARVEL

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GTF file #3

Closed Romeo1-1 closed 1 year ago

Romeo1-1 commented 1 year ago

Hello ! Thank you for this very useful package. The gtf file I used for alignment, the gtf file recommended by CellRanger (refdata-gex-GRCh38-2020-A), did not work correctly when I used "AnnotateSJ.10X and AnnotateGene.10X".

I modified 2 functions to make my GTF file ALSO compatible (the original provided in the example works too). I think these modifications may be useful for other people.

The 2 incompatibilities were "gene_biotype" vs "gene_type" in V9 (i added an if.else check) and chromosomes already having "chr" in V1 (if the string already have "chr", then it does not add "chr".). I didn't notice any difference in runtime.

Thank you,

Rémi Tilmont

wenweixiong commented 1 year ago

Hi Rémi,

Good eye!

I have updated the package (version 2.0.1) on Github to handle both gene_type and gene_biotype attribute labels within the GTF for the AnnotateGenes.10x function.

Thank you!

Sean