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When converting c. HGVS from cDNA to genome coordinates, VEP appears to not take into account alignment gaps, where the cDNA has insertions/deletions vs the reference sequence.
Submission example:
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Hi All,
I am facing a problem regarding Trinotate annotation.
I have generated a transcript annotation file following Trinotate pipeline after de novo transcript using Trinity. In annotation there a…
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Now that we've got about 100k transcripts in our oral argument collection, perhaps a next step would be to add sentiment analysis. I think this is pretty easy stuff these days either through an AI cal…
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Hi,
I am comparing clustering results from CD-HIT and RapClust. One of the characteristics of CD-HIT is that it selects one representative transcript per cluster, while rapclust doesn't. Would it be …
mpaya updated
7 years ago
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Hi，
I used PASA to assemble RNA transcripts and FL transcripts recently. But PASA show the Error at step of cluster assembly :
CMD: PASApipeline-pasa-v2.5.0/scripts/assemble_clusters.dbi -G …
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### Description of feature
Hi,
I recently came across Mikado which is a pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies. Our approach leverages …
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Hi again,
I have a few more burning questions:
1. In the example of ordered-histgrowth from this link (https://github.com/marschall-lab/panacus/blob/main/examples/ordered_pangenome_growth_statis…
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From a EGLH user:
*I used the host address https://ws.zettagenomics.com/cellbase to query version5 of cellbase using pyCellBase. However when I try to get info on gene APOE it doesn’t return the expe…
ghost updated
2 years ago
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The plant I am studying is Chrysanthemum seticuspe, which has a well-assembled genome, but lacks a GTF file. Therefore, I use genome-guided assembly of transcripts. Generally, what is the recommended …
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HI,gpertea.
Histat2 can add XS tag for all read alignments,I have a stranded library (fr-firststrand) data, I use STAR to mapping genome and set options --outSAMstrandField intronMotif which can add …