User: minions-b

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minions-b0
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Posts by minions-b

<prev • 8 results • page 1 of 1 • next >
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Comment: C: filtering reads from plant associated microbes
... Thanks so much for the clear explanations. They help me a lot. :) ...
written 10 months ago by minions-b0
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filtering reads from plant associated microbes
... Hi, I am a newby for RNA-seq and now trying to analysing a transcriptome of two tree species: one with ref. genome and another one without ref. genome. I have some questions that I keep thinking again and again and I hope you can help me to address them. 1. Can you explain me why a ref. genome + ...
rna-seq written 10 months ago by minions-b0
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Comment: C: Lexogen SENSE for de novo assembly?
... Thanks genomax. I will! :) ...
written 13 months ago by minions-b0
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Lexogen SENSE for de novo assembly?
... Hi folks I wonder if anyone would like to share experience with Lexogen SENSE for de novo assembly? I am considering using the kit as it can deal with much lower RNA input (some of my samples have total RNA ca. 50 ng), but I have never tried the kit before. I am working with tree species with a gen ...
assembly next-gen rna-seq written 13 months ago by minions-b0
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Comment: A: Submission of a draft genome with or without repetitive contigs?
... Thanks! I will remove them. :) ...
written 2.1 years ago by minions-b0
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Submission of a draft genome with or without repetitive contigs?
... I have a draft fungal genome assembled/scaffolded with spade (ca. 1,400 scaffolds), which I plan to submit to EMBL. However, ca. 150 of them with very short length (200-500 bp) are identified as repetitive contigs when I used nucmer/funannotate for sanity check before gene prediction. Should I exclu ...
genome written 2.1 years ago by minions-b0 • updated 2.1 years ago by Juke344.9k
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Comment: C: Flat file for functional annotation of draft fungal genome
... Hi Juke-34, Thanks for your reply. I just discovered what could be wrong and it is actually a user-error. It is my first time trying to submit a draft genome.. :( Now I have split GFF3 for each scaffold and am trying to make a flat file for each scaffold individually using EMMLmygff3. Do you have a ...
written 2.1 years ago by minions-b0
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Flat file for functional annotation of draft fungal genome
... Hi folks, I am a wet-lab biologist with limited knowledge about scripting and programming. Now I am preparing a flat file for functional annotation of a draft fungal genome that I have deposited earlier at EMBL. I tried both gff3toembl and emblmygff3, but it seems they both do not like a draft ge ...
embl submission genome functional annotation written 2.1 years ago by minions-b0

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