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How do I access genome coverage using SPADES?
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Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
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Comment: Differential Expression Analysis using DESeq2 in R
by
GenoMax
142k
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?
by
ST
• 0
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.
by
Vijith
▴ 30
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: Raw counts using stringtie
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ahmad.sajad4541
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![stringtie error][1] [1]: /media/images/6475a009-e1a6-412b-8515-a8aec173
Comment: Differential Expression Analysis using DESeq2 in R
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Erina
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![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
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dsull
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My response above was actually partly inspired off of a reading of your paper :)
Comment: Differential Expression Analysis using DESeq2 in R
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ATpoint
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> 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
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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
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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…
Answer: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
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Malat1 correlates with the intronic content and can be used as a nuclear indicator. In this preprint we discuss about this artifact and the…
Comment: How does gene length effect the number of reads mapped
by
dsull
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I wouldn't say it's true that number of reads is linearly proportional to the length of the gene. That's just an assumption that people mak…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★ 1.9k
Using any of the species present would likely result in a resonable annotation set. You could use *Arabidopsis* since it likely has the mos…
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GenoMax
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Have you tried conda install <pkg>=<version> so conda install smalt=0.5.8 <!-- junk -->
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Joe
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Older versions of software are usually available via distribution tools or the websites. It may require a lot of digging, but its almost ce…
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