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Print Differentially Expressed Exons From Dexseq Results
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Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data
by
carolofharvest
▴ 30
Thank you for sharing. What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
Comment: Do I need to go back and filter my long-reads?
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GenoMax
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> I think I will filter the reads ultimately. If your data was not run and basecalled using the same exact version of pore/software for a…
Comment: Raw counts using stringtie
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Ram
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What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
Comment: Do I need to go back and filter my long-reads?
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Ram
43k
> I think you should have the right to delete a question you yourself have submitted If you were to talk to someone, can you make them for…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
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dthorbur
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I don't have any experience using `BRAKER2` so I cannot comment, but I would be extra careful about data you find on non-model organisms. T…
Comment: Differential Expression Analysis using DESeq2 in R
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GenoMax
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You can copy and paste your code and then use `101010` button in the edit window to format it as text to keep it monospaced. For example …
Comment: Same sequencing sample in multiple lanes. How to analyse it?
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ST
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I guess this could really depend on the "counting" strategy, the library complexity and possible lane biases. If e.g., EM is used to guide…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
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Vijith
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Hi dthorbur, thanks for the response. I have run Augustus using Arabidopsis as a species. I would like to know about the suitability of usi…
Comment: How does gene length effect the number of reads mapped
by
dsull
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Alicia Oshlack has done some cool work on this but even the plots in her papers show that TPMs sometimes overcorrect and the relationship i…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![The below image contains the code and result also.][1] [1]: /media/images/96562b96-d508-4f67-96d1-7c71aa17
Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
My response above was actually partly inspired off of a reading of your paper :)
Comment: Differential Expression Analysis using DESeq2 in R
by
ATpoint
82k
> everything is showing equal in environment section. But when I am checking for equalities, it’s showing False No idea what this means. P…
Answer: Analysis of intronic reads included scRNA-seq data
by
t.montserrat.ayuso
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You can calculate the percentage of intronic reads for each cell using the [DropletQC][1] package for R. In this preprint we discuss th…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
I did say almost - obviously things are going to get tricky at gene ends - this is why we have the concept of effective length. Its interst…
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