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gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
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Could not find read type: jaccard #78

Open jialanm opened 1 year ago

jialanm commented 1 year ago

Hi,

I tried to run fds <- calculatePSIValues(fds, types="jaccard", BPPARAM=bpparam()) but keep getting the error: Error in FUN(X[[i]], ...) : Could not find read type: jaccard Calls: calculatePSIValues -> unique -> vapply -> FUN

fds is created from:

    library(FRASER)

    annotation_dat <- data.table(sampleID="{sample_id}", bamFile="{sample_bam_path}", pairedEnd=TRUE)
    settings <- FraserDataSet(colData=annotation_dat, workingDir=".")

    fds <- countRNAData(settings)

I wonder if you could help look into this. Thanks!

ischeller commented 1 year ago

Hi @jialanm , sorry for the late reply, I didn't see the issue earlier. Which FRASER version are you using? Make sure it is > 1.99.0 if you want to use FRASER 2.0 / the Intron Jaccard Index metric.

jialanm commented 1 year ago

Hi Ines,

Thank you for the reply! I am able to use FRASER2 if I install using devtools::install_github('gagneurlab/FRASER', ref='1.99.0', dependencies=TRUE). However, the bioconductor installation does not seem to install the new version even though I specified the version number to be 1.99.0.

Best regards, Jialan

On Wed, Aug 23, 2023 at 9:08 AM Ines Scheller @.***> wrote:

Hi @jialanm https://github.com/jialanm , sorry for the late reply, I didn't see the issue earlier. Which FRASER version are you using? Make sure it is > 1.99.0 if you want to use FRASER 2.0 / the Intron Jaccard Index metric.

— Reply to this email directly, view it on GitHub https://github.com/gagneurlab/FRASER/issues/8#issuecomment-1689934633, or unsubscribe https://github.com/notifications/unsubscribe-auth/BAHDN2XNGP2WVL64USLMYITXWX6FBANCNFSM6AAAAAA2FHXVWY . You are receiving this because you were mentioned.Message ID: @.***>

drewjbeh commented 8 months ago

Hi there,

Could you retry intalling FRASER through Bioconductor. Let us know if it still does not install 1.99.0