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jpromeror / EventPointer

R package for the identification and statistical analysis of alternative splicing events using junction arrays or RNASeq data
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Error in making TxDb object from Bioconductor #9

Closed binasu closed 5 years ago

binasu commented 6 years ago

Hi,

Thanks for this great tool!

I encountered this error in my EventPointer execution (which I'm running in Unix):

Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Error in .make_splicings(exons, cds, stop_codons) : some CDS cannot be mapped to an exon Calls: PrepareBam_EP ... makeTxDbFromGFF -> makeTxDbFromGRanges -> .make_splicings Execution halted

I generated the BAM files with STAR and I'm using the C. elegans WS251 GTF file.

Thanks, Bina

jpromeror commented 6 years ago

Hi @binasu,

Sorry for the delay in the answer!

I've never worked with sequencing files from species different than human, mouse or rat. Can you tell me where you downloaded the GTF file? I will try to replicate the issue.

By the error message it seems that is from the GenomicFeatures dependency. makeTxDbFromGFF -> makeTxDbFromGRanges -> .make_splicings

I'll let you know as soon as I have updates.

Best regards,

jpromeror commented 5 years ago

Hello @binasu,

I will close the issue as there has been no response or comment since July.

Best,

jadeeerose commented 3 years ago

Were you able to resolve this? I am getting the same error using a bacterial genome.