User: BioBing

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BioBing80
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Posts by BioBing

<prev • 29 results • page 1 of 3 • next >
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Answer: A: Best practises RNAseq - Sleuth vs. NA's in annotation
... Thank you both for very good and useful answers - it is tricky to figure out what is the "best practice", but I think I will add in the Trinity names, because some of them are highly significantly expressed. ...
written 16 days ago by BioBing80
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Best practises RNAseq - Sleuth vs. NA's in annotation
... Hi all, Currently, I am working on my very first RNAseq study and have met a dilemma where inputs from more experienced bioinformaticians would be amazing. For a differential gene expression study in a non-model organism, a de novo reference transcriptome was assembled from 300 M reads in Trinity ...
R rna-seq written 17 days ago by BioBing80
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Kallisto/Sleuth - issue when using own annotations in the sleuth_prep() function
... Hi all, Hoping that some of you are familiar with Kallisto/Sleuth and might be able to help me out. I am analyzing transcripts from a non-model species with triplicates of a control condition and two different treatments. For annotation, I have used Diamond (none of the Ensembl genomes are close ...
R sleuth kallisto rna-seq written 4 weeks ago by BioBing80
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Comment: C: How to annotate only selected genes on a heatmap
... Hi Michael, Yes, I agree - my approach is kinda messy :-) But it was how I got it to work, and I just wanted to share it in a case of it could be helpful in some way. Ahh! I just realized I misunderstood the question, my fault. I thought the question was about getting annotations into a heatmap of ...
written 4 weeks ago by BioBing80
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Comment: C: BLAST IDs into gene names? (Diamond)
... I think I already did that? ...
written 4 weeks ago by BioBing80
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Answer: A: How to annotate only selected genes on a heatmap
... Hi h.fushimi.x689, When you write annotate genes, do you mean transcripts? (if so, there is a risk that you will have multiple transcripts that are encoded by the same gene) This is a quick and dirty method that I have used to get a "quick" overview of my transcripts: 1) Extract the IDs for the t ...
written 4 weeks ago by BioBing80
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Comment: C: BLAST IDs into gene names? (Diamond)
... Thank you! That option is also available for "my" version! This is just what I needed! ...
written 5 weeks ago by BioBing80
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Comment: C: BLAST IDs into gene names? (Diamond)
... That sounds interesting! I will definitely check it out - do you know if it is able to run "bulk IDs" as well? or is it only one at a time? ...
written 5 weeks ago by BioBing80
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Comment: C: BLAST IDs into gene names? (Diamond)
... I would love to use Trinotate! :-) But unfortunately, I am only a guest on the server that I am using for data analyses and have no permissions to install Trinotate and its dependencies (my laptop is not able to run the analyses on its own without exploding ;-) or at least it sounds like that when ...
written 5 weeks ago by BioBing80
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Comment: C: BLAST IDs into gene names? (Diamond)
... I am working with a non-model species with no available genome or transcriptome. I did a very deep sequencing and did a *de novo* assembly with Trinity. None of the available Ensembl references are close to the species I am working on. I ran a Diamond annotation on the assembled Trinity transcript ...
written 5 weeks ago by BioBing80

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