Moderator: lieven.sterck

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lieven.sterck5.5k
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Posts by lieven.sterck

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Comment: C: How to retrieve the original protein code before it has been published on NCBI a
... I had a quick look at the NCBI ones and it turns out that their IDs are derived from a new annotation round they performed with their inhouse pipeline. It is thus very likely that there will not exists a nice 1-to-1 conversion table for the IDs as the genes will differ. One option you have is to c ...
written 12 hours ago by lieven.sterck5.5k
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Comment: C: How to retrieve the original protein code before it has been published on NCBI a
... is there any specific reason you want to use the NCBI one? why not use the version they offer for download at their olivegenome.org website (or ORCAE or pythozome, ... ) ? ...
written 1 day ago by lieven.sterck5.5k
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Comment: C: Best Genome Assembler and Genome Annotation tools and pipelines
... little confused about your question: it sounds like you already have lots of things done already (eg. you seem to already have an assembly). So what's the goal of looking for other software, (what have you used so far btw), are you not satisfied with the current results? ...
written 6 days ago by lieven.sterck5.5k
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Comment: C: BRAKER miss some genes despite of RNA-Seq evindence
... apart from what https://www.biostars.org/u/12371/ already mentioned, you have to keep in mind that all these tools (approaches) have the goal to correctly predict as much genes as possible. This of course does not mean that all genes will be correctly predicted (if at all) but that the majority of t ...
written 8 days ago by lieven.sterck5.5k
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Comment: C: Advices for Single Cell analysis. Softwares to go ?
... perhaps not fully up-to-date anymore but still a good starting point : [https://github.com/seandavi/awesome-single-cell][1] [1]: https://github.com/seandavi/awesome-single-cell ...
written 11 days ago by lieven.sterck5.5k
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Comment: C: Why Ks value is NA in KaKs calculator
... at first sight there are a few things going on here: - for KaKs analysis you need two sequences (can we assume the ones you posted are actually two sequences) - the sequence needs to be correctly aligned, for Ks analysis that should even be codon-aware alignment - normally you would expec ...
written 11 days ago by lieven.sterck5.5k
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Comment: C: Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcri
... That's debatable ;) , it uses assumptions/approach which are nowadays considered as being outdated (eg FPKm values ... ) Of course I agree that one should not ignore the (well-annotated) human transcriptome but OP specifically asked an approach to identify novel transcripts. In the context of not h ...
written 18 days ago by lieven.sterck5.5k
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Comment: C: Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcri
... well yes and no. With your option 2 you will never find any new transcript as you only look at the known ones. Option 1 is your only valid option to find anything new (== un-annotated). I could kinda agree that Trinity might not be the best option (though also not the worst one either and it will ...
written 19 days ago by lieven.sterck5.5k
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Answer: A: Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcri
... option 1 ! (though the title of your post does not really covers this option) as https://www.biostars.org/u/24526/ already mentioned. if you use the hg38 known transcriptome (your option 2) than indeed you wont find any novel transcripts. You might find "known" genes that lack any functional annota ...
written 21 days ago by lieven.sterck5.5k
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Answer: A: How to calculate overlap of peptides between different categories to create Ven
... if you are looking for exact mactches (so no peptide can be subset of another) you can use your lists as such as input for [DrawVenn][1] . It's an online tool for drawing venn diagrams [1]: http://bioinformatics.psb.ugent.be/webtools/Venn/ ...
written 21 days ago by lieven.sterck5.5k

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