I am looking for a FASTA file and GTF file that I can use to align my RNA seq (Hiseq) data and then anotate differential expressed genes. I looked at Xebase database, Ensembel but could not find these files. Can someone point me to a DB where I can find X tropicalis FASTA and GTF/ Gff files.
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Ensembl download page
Species table in the middle of page. Type 'Xenopus' in the Filter box (right side of table header). There are links to download whole genome FASTA, cDNA FASTA, CDS FASTA, etc as well as GTF/GFF3 annotation files.
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by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
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