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Comment: How can I map coordinates between two strains of yeast?
by
dthorbur
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840
I think that is an alternative to a synteny analysis, but I only know liftover in terms of annotations. OP asks for "coordinates between th…
Comment: Bowtie mapping for single_end read
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ATpoint
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I am sceptical any tweaking of parameters will make a notable difference. Parameters in bowtie are very good at default, and given it's ChI…
Comment: How can I map coordinates between two strains of yeast?
by
cmdcolin
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3.4k
would something like liftover not be recommended? honest question
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
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840
That's good. But I still suspect this data might be really difficult to analyse. I have a handful of suggestions I would do to assess wheth…
Comment: Identify clusters of populations based on gene expression
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dthorbur
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840
One gene might not be enough data to "cluster" based on expression. Unless I'm missing something, that would just be breaking a single cont…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
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Yes, I performed ribosome depletion using an RNAse H based method.
Comment: Circular genome browser
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cmdcolin
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that's great to hear. one "proxy" for interactive is looking at the JS based tools, many are web based and interactive as a result. I have …
Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
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TC_Chang
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Hi jv,
Thank you for your reply. Basically, I'm trying to generate the figure shown below with two different y-axis scales.
Any suggestio…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴
840
I don't have a suggestion for low yield DE analyses, but I am curious about the samples. Did you conduct any ribo-depletion steps prior to …
Answer: How can I map coordinates between two strains of yeast?
by
dthorbur
▴
840
It sounds like you are looking for synteny between the two genomes. I'm assuming they are assembled, but that may not be the case. If so, […
Comment: Identify clusters of populations based on gene expression
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Nitin Narwade
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Why don't you just plot it on your UMAP If it is specific to one cluster/sub-population you should get a relatively high expression in that…
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GenoMax
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Default `task` option is `megablast` for `blastn` which looks for `highly similar sequences` compared to `blastn` which is looking for `som…
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https://www.biostars.org/u/14684/ may comment on this but it may be the order of operations that is causing this. After the `tpe` is applie…
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colindaven
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Inspector (only for long reads) and Merqury for short reads are also pretty good methods for doing a QC of your assembly.
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GenoMax
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> why I have soo many multimapping reads?
That is a characteristic of the libraries. Not much you can do at this point in process. Just ha…
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