User: viktoria.c.karlsson

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Posts by viktoria.c.karlsson

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Comment: C: Make a GFF-file compatible for reference database
... OK, thank you for your response :) ...
written 8 months ago by viktoria.c.karlsson0
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Comment: C: Make a GFF-file compatible for reference database
... Do you know if I can just delete the attributes for the CDS feature, or will that impact the counts I get? ...
written 8 months ago by viktoria.c.karlsson0
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Comment: C: Make a GFF-file compatible for reference database
... Yep. I think the problem is that some of the CDS-features have the same attribute value. For this script that does not count as redundancy. Though I can not find away to make them unique. ...
written 8 months ago by viktoria.c.karlsson0
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Comment: C: Make a GFF-file compatible for reference database
... I really thought this would solve it, but now I have tried both the script you recomended and the one called remove redundants, and mysql still does not accept the file. When I run the redundant-script it says that there are no redundancies. I do not get this at all... ...
written 8 months ago by viktoria.c.karlsson0
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Comment: C: Make a GFF-file compatible for reference database
... No worries! No difference I'm afraid. It gives me the same error. The weird thing is that their warn for this in the readme file, but there is no solution given... ...
written 8 months ago by viktoria.c.karlsson0
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Comment: C: Make a GFF-file compatible for reference database
... You mean just the same file but zipped? Does not work... Thanks anyway! ...
written 8 months ago by viktoria.c.karlsson0
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Comment: C: Make a GFF-file compatible for reference database
... I am using the one called just Mus_musculus.GRCm38.99.gff3 and the primary assembly as reference genome. So I guess that is not the problem... ...
written 8 months ago by viktoria.c.karlsson0
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Make a GFF-file compatible for reference database
... I am doing an mRNA analysis (mRNA from mice) and want to use GENE-counter for getting raw counts. The manual says that I need a reference genome and a annotation file in GFF3-format, which I will use to create a reference database in MySQL. Now I have tried reference and GFF from both refseq (from N ...
ensembl gff mysql rna-seq gene-counter written 8 months ago by viktoria.c.karlsson0
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Extract data from CATALYST-plots after clustering (in R)
... Hi! I want to do a cluster analysis of mass cytometri data, using R. I am planning to follow this workflow: https://bioconductor.org/packages/release/workflows/vignettes/cytofWorkflow/inst/doc/cytofWorkflow.html#visual-representation-with-umap However, I have a visual impairment and use a screen ...
R bioconductor cluster analysis written 9 months ago by viktoria.c.karlsson0 • updated 9 months ago by zx87549.7k

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