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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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GFF for SK1 fasta #49

Closed cathoderaymission closed 4 years ago

cathoderaymission commented 4 years ago

I am unable to find the exact fasta sequence file for the SK1 strain you recently added. Can you provide the source? I would like to get the GFF file for the transcriptome.

Thanks!

cathoderaymission commented 4 years ago

I found the genome under ftp://ftp.sanger.ac.uk/pub/users/dmc/yeast/latest/cere_assemblies.tgz however the transcriptome contained in the GFF records goes over the bounds for the sequence lengths for things like the YIR023C-A gene in chromosome 9.

Did the epinano project use the sk1 genome you recently added under references or the transcriptome for alignment?

Huanle commented 4 years ago

Hi @cathoderaymission,

We used SK1 genome for alignment.

Huanle commented 4 years ago

I found the genome under ftp://ftp.sanger.ac.uk/pub/users/dmc/yeast/latest/cere_assemblies.tgz however the transcriptome contained in the GFF records goes over the bounds for the sequence lengths for things like the YIR023C-A gene in chromosome 9.

Did the epinano project use the sk1 genome you recently added under references or the transcriptome for alignment?

You might want to try to get the SK1 genome annotation from https://software.broadinstitute.org/software/igv/Genomes