User: lieven.sterck

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lieven.sterck1.4k
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Belgium, Ghent, VIB
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Posts by lieven.sterck

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Comment: C: What is the difference between complete genome and chromosome at NCBI? Why these
... can you add the context where these terms are mentioned? ...
written 12 hours ago by lieven.sterck1.4k
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Comment: C: Decision on no. and type of libraries to be generated for plant genome assembly
... from having done similar kind of projects previously. People tend to transfer what worked for genome X to genome Y . Anyway, I think estimated genome size is the main factor here (tightly linked to available funding) ...
written 2 days ago by lieven.sterck1.4k
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Comment: C: Decision on no. and type of libraries to be generated for plant genome assembly
... I don't think there is a rule-set to calculate this. it's usually based on experience and gut feeling ;) (and some prior knowledge on that specific genome/species ) ...
written 3 days ago by lieven.sterck1.4k
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Comment: C: STAR-HT-Seq/featureCount got much more gene expression count than RSEM did
... I'm agreeing with https://www.biostars.org/u/7403/ here but he could be using the bam output from RSEM and (re-)use that as a bam input file for htseq-count, no? ...
written 3 days ago by lieven.sterck1.4k
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Comment: C: getting a combination of all predicted genes
... you bluntly want to merge the 2 predictions together? I'm not convinced this is the way forward as this does not guarantee the 'merged' models will make any biological sense. But I'm guessing you might know that already. So what is the goal of all this? ...
written 4 days ago by lieven.sterck1.4k
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Comment: C: SSPACE assembly merger
... Perhaps there is nothing to scaffold based on the data you provided? Do you have reads aligning to 2 different contigs? ...
written 4 days ago by lieven.sterck1.4k
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Comment: C: Finding a gene of interest in contigs from a transcriptome sequencing.
... the same species or other species of my answer is equally (if not more) important ! Do think about what data you have. ...
written 5 days ago by lieven.sterck1.4k
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Answer: A: Finding a gene of interest in contigs from a transcriptome sequencing.
... Blast is gonna be your tool of choice! Is your gene sequence (nucleotides?) of the same species as the one of the transcriptome? When yes: use blastn ; if no: use tblastx . ...
written 7 days ago by lieven.sterck1.4k
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Comment: C: predict UTRs using PASA
... 138 UTRs out of how many genes? perhaps there simply is not more data support for UTRs ? ...
written 8 days ago by lieven.sterck1.4k
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Comment: C: Combining Maker and Blast2Go
... perhaps I'm misinterpreting the graph , but does it not say there are only ~600 genes with a GO (or does the mapping bar also counts for GO?) ...
written 8 days ago by lieven.sterck1.4k

Latest awards to lieven.sterck

Scholar 18 days ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 19 days ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 19 days ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
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Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: converting RSEM bam output into sam files for DEseq?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 11 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Teacher 3 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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Scholar 3 months ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 3 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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