Question: Mapping C albicans supercontigs to chromosomes
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gravatar for Samuel
13 days ago by
Samuel10
Samuel10 wrote:

Hello,

Apologies if this is a silly questions, I am still new to bioinformatics and learning as I go. I am trying to generate a BDG file to visualise RNA transcription levels of WT SC5314 C.albicans in IGV. I am following this manual. I understand that i will need a GTF/GFF file to serve as a cDNA library that reflect the transcriptome. I was able to find the file in both CGD and EnsemblFungi. However, the format of the files seems to be incompatible with STAR and the pipeline in general. The GTF file from CGD does not specify exons and the geneID are the same as the transcript ID which i heard will cause some problem. On the other hand, the Ensembl GFF3 file has the transcripts mapped to supercontigs rather than chromosome but provide exon data.

I am wondering if there is a way to map the supercontigs from the Ensemble GFF3 file into chromosomes to make it into a format i can use.

Thanks in advance

c_albicans rna-seq • 69 views
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