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Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
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70
Hi Juke,
I am trying to install it and I can't.
![enter image description here][1]
[1]: /media/images/bc08978b-10f7-4666-b385-57807b…
Comment: comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or
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cmo
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I agree with you, Mensur, that the GTDB is arguably more reliable and comprehensive than NCBI. However, due to the relative greater longevi…
Comment: how to select peaks at not transcribed genes
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Lila M
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rigth, it is a ChIP seq analysis
Comment: how to select peaks at not transcribed genes
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ATpoint
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Which type data are we talking about? What was the experiment? There are literally no details in this question right now. It the assay meas…
Comment: MASURCA output
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kilcdincer
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Thank you. I understood ploidy part.
My genome is supposed to belong to diploid Candida albicans. And genome size of diploid Candida alb…
Answer: How to combine 2 incomplete GTF
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Juke34
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To give more precision to the @genomax comment:
`agat_sp_compare_annotations.pl` will tell you the differences.
Then you can choose to …
Comment: GSEA for RNA_seq dataset
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ATpoint
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No problem. I am not really familiar with what the GSEA implementation from the Broad institute does. I personally use fgsea from Bioconduc…
Comment: how to select peaks at not transcribed genes
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Lila M
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910
you mean in the call peaks? And what are those 232 not annotated peaks?aren't they tss associated to not transcribed genes?
Comment: How to combine 2 incomplete GTF
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GenoMax
99k
Compare annotation tool `agat_sp_compare_annotations.pl` from [AGAT toolkit][1]. Install [**AGAT**][2] using `conda`.
[1]: https://gith…
Comment: GSEA for RNA_seq dataset
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1961012
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I am really sorry for asking for clarification because I am a beginner.
I already used all genes (normalized and filtered) for GSEA using …
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aka
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I work in a research laboratory that has specific demands that make the general pipeline not fit, I have to create it from scratch, but tha…
Comment: Extract chromosome 1 - 22 fasta file
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shubhamkumbhar420
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Thank you for your response! It worked !!!
Answer: How to combine 2 incomplete GTF
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Michael Dondrup
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I made this perl script to compare two GFF files. It might be useful after some modifications (changing GFF version to 2?). Needs BioPerl i…
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