Moderator: lieven.sterck

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lieven.sterck8.6k
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Posts by lieven.sterck

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Comment: C: Using featureCounts on paired-end reads aligned with HISAT2 resulting in 0 assig
... not sure this is the cause of the issue(s), but in the `samtools` sort step, make sure you order them on name rather than position. ...
written 10 hours ago by lieven.sterck8.6k
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Comment: C: Looking for easy to use eukaryotic genome annotation pipeline?
... good question, perhaps ask https://www.biostars.org/u/12371/ ;-) often people rely on 'bacterial' approaches as transcriptome is (or should be ) all single frame, single "exon" (== resembling prokaryotic ) If I remember correctly , in the original Trapid paper there was a comparison with other too ...
written 1 day ago by lieven.sterck8.6k
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Comment: C: Looking for easy to use eukaryotic genome annotation pipeline?
... possibly, though I then wonder which pipelines you came across before, as usually Maker is one of the first to pop up. ...
written 1 day ago by lieven.sterck8.6k
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Comment: C: Looking for easy to use eukaryotic genome annotation pipeline?
... that must have been an eye-opener indeed when you come from the bacterial (genome annotation) field :) . anyway, what pipelines have you come across? and why don't you 'like' them? part of which these pipelines are convoluted and sometimes complex is because eukaryotic genome annotation is complex ...
written 1 day ago by lieven.sterck8.6k
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Comment: C: De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
... Getting and annotating the genome will indeed give you the highest quality annotation for this species, though this comes will seriously additional work!! and is not a route you want to embark on unprepared, unfortunately. For annotating the current transcriptome, and given you do not have much exp ...
written 2 days ago by lieven.sterck8.6k
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Answer: A: Question: Convert .SRA to .FASTA
... You can use following program from [BBMap suite][1]. reformat.sh in=your.fq out=your.fa This will convert your fastq files into fasta format. educational note: you could have find this easily by doing a search on google (and/or limiting to biostars.org) [1]: https://jgi.doe.gov/data-and-t ...
written 2 days ago by lieven.sterck8.6k
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Comment: C: CODEML: Ideal setting for generating dn/ds values for a gene family within a spe
... I don't see any immediate reasons why you would have to use a different approach for a within species or between species analysis. Those values are calculated on a per gene basis, regardless of where those genes come from. This does not mean you might get more reliable results when you include some ...
written 4 days ago by lieven.sterck8.6k
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Comment: C: De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
... correct. I was going to ask how crucial this 'assembly' is. It likely can be improved but that will require serious additional work, which might not be worth the effort, depending on the goal. ...
written 4 days ago by lieven.sterck8.6k
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Comment: C: De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
... yes, indeed. it is a bit of a grey zone as I don't think they all will be genuine isoforms (you might also pick up allelic variations , from within an individual as well as from different individuals), but technically they pose the same issue for your mapping result. Well, that alignment result ce ...
written 4 days ago by lieven.sterck8.6k
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Comment: C: De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
... > Is this a sign that the assembled transcriptome is quite redundant? well, I would say yes. You can also spot this from the BUSCO result: high rate of duplication! It seems you have quite some sequence variability in your transcripts (which can be explained biologically as well here, multiple ...
written 5 days ago by lieven.sterck8.6k

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