Please help

[bian...@gmx.de]

To whom it may concern,

My name is Bianka, and I study bioinformatics in Germany.

As part of my bachelor thesis, I am investigating alternative splicing in fungi and would like to add a new species (Magnaporthe oryzae). In your notes, I read that this is only possible to analyse 3' Affymetrix and Gene 1.0 arrays. Can you help me with this?

Sincerely,

Bianka

 

 

[Nathan Salomonis]

Hi Bianka,

Actually, we primarily support RNA-Seq based analyses for species supported in Ensembl. In this case, Magnaporthe oryzae (https://fungi.ensembl.org/Magnaporthe_oryzae/Info/Index) most recent Ensembl supported database is Fungi50. To add support for this in AltAnalyze from the source code, the command is:

python AltAnalyze.py --update all --version Fungi50 --species Mo --platform RNASeq --force yes

python GO_Elite.py --update Ensembl --species Mo --system all --update Ontology --version Fungi50

You would run this command after indicating in the Config folder files that the Magnaporthe oryzae corresponds to the species code Mo (species.txt, species_all.txt, species_archive.txt, goelite_species.txt) and that this species corresponds to fungi protein isoforms (default-files.csv), as done in the attached files.

Running this command produces a folder within the AltAnalyze directory AltDatabase, which has been zipped and linked to below. Simply replace the attached Config folder files in your version of AltAnalyze (source code or compiled version downloaded from the website) and place the unzipped EnsMart50 folder (see below Google Drive link) into the AltDatabase folder and you should be ready to pseudo-align FASTQ file, run single-cell unsupervised analyses, differential expression, pathway enrichment, differential splicing and more. 

https://drive.google.com/file/d/1BBHEbXdfQfus3Mj9LQU3NUyWanYwb4mH/view?usp=sharing

Let us know if you have any questions. 

Best,

Nathan

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