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Recent Replies
Comment: Contigs to chromosomes annotation
by
GenoMax
129k
I would still recommend using `minimap2` and aligning against reference. It should go pretty fast. You can either work with PAF (default) f…
Comment: Diff Bind Questions
by
Ram
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I've moved this to a comment as it does not directly answer OP's question.
Comment: Diff Bind Questions
by
Daniel
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30
I'm very new myself and there's plenty of people who can answer your question better than I can, but here is a resource I found extremely h…
Comment: Contigs to chromosomes annotation
by
alexandru.bologa.marian
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If the number of contigs was so small I would manually check each alignment and edit the header of each contig,inserting the corresponding …
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Ram
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Do not post on multiple fora just because you want a fast response, it's plain rude. At least point to the other post so we know you're ask…
Comment: Limma returned only positive logFC values
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melissachua90
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No the library sizes across conditions should be relatively homogenous because it's from the same dataset. I clustered the samples into sub…
Comment: Limma returned only positive logFC values
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LChart
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It shouldn't, unless there's a misspecification in design. Is it the case that the library sizes are very different between the conditions …
Comment: Contigs to chromosomes annotation
by
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For a pure contig to Dmel chromosome BLAST should be OK.
I am fan of LAST because it is fairly easy to convert MAF to SAM/BAM and then vi…
Comment: Contigs to chromosomes annotation
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GenoMax
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How many contigs do you have? If the contigs are ~2x number of Drosophila chromosomes (meaning you have long/large contigs) then using a lo…
Comment: Contigs to chromosomes annotation
by
alexandru.bologa.marian
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Thank you for your answer!
It would be wrong just to BLAST all the contigs from the draft assembly against each reference chromosome of D.…
Comment: Limma returned only positive logFC values
by
melissachua90
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Several hundred to 10000 DEGs.
Would normalization affect logFC?
Answer: Contigs to chromosomes annotation
by
Darked89
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Not sure if it is the easiest, but you can map your new assembly to i.e. Dmel genome using LAST:
* www: https://gitlab.com/mcfrith/last …
Answer: Gene prediction software
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Darked89
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How complete/polished is your catfish genome assembly?
Also: do you have some good quality RNA-Seq?
With a draft genome it would be…
Comment: Limma returned only positive logFC values
by
LChart
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It'd be helpful to know how many differentially expressed genes there are. If you've got a handful and they're all upregulated, I wouldn't …
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Ram
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Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21118/how-to-calculate-the-variant-allelic-fraction-vaf
OP,…
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