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Determine what information is needed in a GFF file and write a diagnostic check for this. The Sequence Ontology Consortium wrote the standard for GFF, and they have an online GFF checker written in Pe…
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NotationConverter.normalizeGenomicLocation(GenomicLocation genomicLocation) will strip a common nucleotide prefix from a Genomic Location, removing invariant nucleotides at the start of the variant fr…
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Good morning,
I'm contacting you for a question on how to define the neutral model. My situation is the following: I've generated multiple genome alignments for 5 assemblies using cactus. I would lik…
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En tant que bio-informaticien, je veux pouvoir transmettre mes fichiers de séquencements de génome et d'exômes et exécuter un workflow d'alignement, d'annotation ainsi que de collectionner les métriqu…
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Hi @tropfenameimer,
I need to create the mouse database with an additional motif.
In order to run create_cisTarget_databases the procedure say that you need the motif collection and the FASTA file.
…
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### Publication and Data Information
Publication is now out and should link to analysis record with title "Castanea mollissima v3.2 and 4.2 - Reference Genome"
https://link.springer.com/article/10.…
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Hello there,
Thank you for a wonderful software. I am trying to use finder with RNAseq data which resides on my local machine. From the logs it seems that its actually not running the STAR alignme…
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Is it possible to add the genome positions from the predicted transcript ?
I have already populated Trinotate.sqlite with the Trinotate_report.xls.
If I setup a file "chr_positions" containing a t…
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Dear Brian,
I am annotating a lizard genome by combining GeMoMa (Homology-based), AUGUSTUS (ab initio prediction), and StringTie (transcription-based). Since the transcription was from only uterus …
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I downloaded the latest version of starfusion singularity image
star-fusion.v1.11.1.simg
Then used the following command to generate a Rat novergicus library with the latest ensembl references a…