User: Nico80

gravatar for Nico80
Nico8020
Reputation:
20
Status:
New User
Location:
University of Edinburgh, UK
Last seen:
19 hours ago
Joined:
10 years, 6 months ago
Email:
r************@gmail.com

:)

Posts by Nico80

<prev • 8 results • page 1 of 1 • next >
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Comment: C: TF binding site analysis - how to filter hits?
... Thank you very much, Alex, I will read through that and see if I can get my way through it! ...
written 16 days ago by Nico8020
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TF binding site analysis - how to filter hits?
... I have a list of genes and I am trying to determine whether they contain specific TF binding sites in their promoter region. I am retrieving 3kb upstream of TSS using `getPromoterSeq` and then use `TFBSTools` and `JASPAR2020` to look for TF binding sites. To simplify things, let's take an example ...
R jaspar tfbstools written 16 days ago by Nico8020 • updated 16 days ago by Alex Reynolds31k
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Comment: C: Strategies for merging RNAseq datasets
... Yes, I know how to add those in DESeq2, thank you. What I meant with the random effect comment, is that as far as I am aware, DESeq2 only allows for fixed effects, while batch is really a random effect in this type of design. ...
written 6 months ago by Nico8020
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Comment: C: Strategies for merging RNAseq datasets
... Thank you ATpoint, that seems like a good place to start! ...
written 6 months ago by Nico8020
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Comment: C: Strategies for merging RNAseq datasets
... Thank you, Asaf. In theory, the controls should be very similar (same tissue from mice of the same strain/sex/age etc). I will try adding a batch effect in the model, although I don't know whether there is a way of putting that as a random effect in DESeq2 (I seem to recall this not being an option) ...
written 6 months ago by Nico8020
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Strategies for merging RNAseq datasets
... I have two RNAseq experiments that were run on the same type of samples, treated in two different ways and sampled over time. So, experiment 1 has experimental groups: Control (untreated) - Treatment A - 1 week recovery from treatment A - 4 weeks recovery from treatment A Experiment 2 is Control ...
R rna-seq written 6 months ago by Nico8020 • updated 6 months ago by Asaf8.5k
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Comment: C: Which genome files to use for STAR?
... Thank you Benn, just out of curiosity, could you confirm whether my understanding of what the different files are is correct? ...
written 19 months ago by Nico8020
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Which genome files to use for STAR?
... I am trying to build a genome index for use with STAR, and I am a bit confused on which files I should use. According to the [STAR manual](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) (§2.2.1) > It is strongly recommended to include major chromosomes (e.g., for human chr1-2 ...
genome alignment star written 19 months ago by Nico8020

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Popular Question 6 months ago, created a question with more than 1,000 views. For Which genome files to use for STAR?

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