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Recent Replies
Comment: How does gene length effect the number of reads mapped
by
dsull
★
5.9k
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
by
ahmad.sajad4541
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0
![stringtie error][1]
[1]: /media/images/6475a009-e1a6-412b-8515-a8aec173
Answer: Differential Expression Analysis using DESeq2 in R
by
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
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
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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
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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
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dsull
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5.9k
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.
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dthorbur
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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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Have you tried
conda install <pkg>=<version>
so
conda install smalt=0.5.8
<!-- junk -->
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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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Thank you very much for sharing your advice. Yes, it definitely makes sense that with the use of deep learning, models would learn normalis…
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I didn't use the same tool as in the paper...
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eebloom
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Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
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