Moderator: lieven.sterck

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lieven.sterck7.8k
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Posts by lieven.sterck

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Comment: C: Retrieving assembly scaffold length information without downloading the sequence
... you will need to provide more details if you want to receive valuable answers. Eg. which assembly? where are you 'downloading' it from? Please go through https://www.biostars.org/p/357878/ and then consider editing your question. ...
written 1 hour ago by lieven.sterck7.8k
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Comment: C: How to extract sequence of a specific feature in gff
... have you looked into this toolbox: https://github.com/NBISweden/AGAT , likely it will hold some function that does this. ...
written 21 hours ago by lieven.sterck7.8k
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Answer: A: How to distinguish between insertion and assembly error in transcripts?
... One way to check this is to align your input reads back to the assembled transcripts and inspect the coverage. If the coverage of the 'inserted' part is deviating much from the surroundings it might indeed be an artefact . However you most likely will never be a 100% sure as it could just as well b ...
written 4 days ago by lieven.sterck7.8k
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Comment: C: Versioning of Blast DB and Reproducible Research
... In that case you should not only keep track of the DB itself but also of the blast binaries of course (much more feasible than the DBs them self though) ...
written 4 days ago by lieven.sterck7.8k
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Comment: C: Versioning of Blast DB and Reproducible Research
... OP did not (yet) indeed. I alluded to it, but no reply on it (yet) ...
written 4 days ago by lieven.sterck7.8k
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Comment: C: Transcript or cds for phylogenetic tree ?
... well, yes and no. I meant that the biological constraints put into place by evolution mainly play on those kind of sequences. As a consequence the algorithms that model/analyse those things are also best performing (optimised) on those sequences indeed. ...
written 4 days ago by lieven.sterck7.8k
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Answer: A: Transcript or cds for phylogenetic tree ?
... It does matter. Go for the CDS (or the protein is even better). Evolutionary constraints/conservation works mainly on those sequences (and less on the UTR, which is what you add when using the complete mRNA/transcripts). If in the unlikely event that the CDS/protein does not give you enough 'reso ...
written 5 days ago by lieven.sterck7.8k
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Answer: A: Versioning of Blast DB and Reproducible Research
... as said above, good to hear you care about reproducible science! However, I feel it's also important to be somewhat pragmatic in this. As also @genomax said above, there are often a whole bunch of technical limitations coming into play here. Along the same line one should also keep track (and keep ...
written 5 days ago by lieven.sterck7.8k
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Comment: C: Versioning of Blast DB and Reproducible Research
... you're absolutely right, a bit of a tricky situation/issue indeed. But nonetheless happy to hear you care about reproducible science! what DB are we talking here btw? something custom of something like `nr` or `nt` or such ? ...
written 5 days ago by lieven.sterck7.8k
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Comment: C: Calling Exon Skipping Events from RNA-Seq
... in this [paper][1] they developed a tool called `findAS`, not sure if applicable for your situation. more in general, I suggest to have a look at (google for) alternative splicing detection tools [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574008/ ...
written 6 days ago by lieven.sterck7.8k

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Teacher 4 days ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Teacher 4 days ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 4 days ago, created an answer that has been accepted. For A: List of all GO terms
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Teacher 14 days ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
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Scholar 26 days ago, created an answer that has been accepted. For A: List of all GO terms
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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 5 weeks ago, created an answer that has been accepted. For A: List of all GO terms
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Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
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