lacking reference transcriptome
I am an undergraduate student who is under a professor's research regarding transcriptomic analysis of Abrus precatorius, but now my progress is stuck because of the lacking reference data for enrichment. Even when I wanted to match it with Arabidopsis thaliana as an ortholog, the enrichment is still unavailable. Has anyone gone through this problem with a novel species? Thank you in advance.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Job: Tenure Track Position for Computational Biologist
written by indiren.pillay •
-
Job: Junior Faculty at University College Dublin (Ireland), Biology All Areas
written by rory.johnson •
-
Job: Postgraduate Student in Bioinformatics and Liver Cancer Genomics
written by waihungh •
-
Job: Postgraduate student in Bioinformatics and Cancer Genomics
written by waihungh •
-
Job: Tenure Track Position, Instructor in Bioinformatics, Department of Biochemistry & Molecular Bi…
written by jlytton •
-
Job: PhD Studentship: Comparative approaches to genomic and transcriptomic characterisation of Duch…
written by androniki.psifidi •
-
Job: 3-year fully funded PhD studentship in bioinformatics at the Royal Veterinary College London
written by Gunnar Schulze •
-
Job: Assistant Professor of Biology - Ecologist, Colby College - Waterville, ME, USA
written by mlburns •
-
Job: Assistant Professor of Biology Computational Biologist/ Genomicist Colby College Waterville, …
written by artilden •
-
Job: (Senior) Research Associate In Bioinformatics And Comparative Genomics At Ucl, London
written by Christophe Dessimoz
What does that mean? A genome reference is available for
Abrus precatoriusfrom NCBI: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/935/025/GCF_003935025.1_Abrus_2018/Take a look at the README.txt file. You will likely want to use https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/935/025/GCF_003935025.1_Abrus_2018/GCF_003935025.1_Abrus_2018_cds_from_genomic.fna.gz as the transcriptome.
Are you trying to do RNA-seq analysis ? Do you have RNA-seq reads from Illumina in fastq format ?
Talk to your supervisor and ask for guidance. If you need strangers on the internet for such basic tasks and your group has no support for you I would reconsider whether spending time with this group is a good investment of time. Saying this in your best interest. Undergraduates should follow some guided research efforts, not figuring it all out themselves. Lots of time for that in a PhD.