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Recent Replies
Comment: Salmon index not progressing
by
Michael
53k
Are you a student or employe at a university or research institute? In this case it is worth checking with your IT department if there is a…
Comment: Salmon index not progressing
by
Michael
53k
I think you should kill one of the processes, possibly the decoy one. Also keep an eye on the CPU temperature and the kernel_task. If CPU u…
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
We use the OmniATAC protocol, which is an enhanced version. Celltype usually does not matter. Based on many years with this assay I can say…
Comment: ATAC-seq troubleshoot - Just Noise
by
vk
▴
40
We used U2OS cells and followed the protocol given [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/).
Answer: How to check RNAseq support for annotated genes?
by
Juke34
8.2k
You could also do transcriptome assembly and then map the transcripts on the annotation via MAKER that will add an AED score for concordanc…
Answer: How to check RNAseq support for annotated genes?
by
Michael
53k
To check for support of gene models by RNAseq, there are several proven workflows. I recommend using them all:
- Standard RNAseq analysis …
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
Yes, definitely lots of noise and few peaks for such an experiment. Which celltype is that, and which lab protocol did you use?
Comment: DESeq2 analysis using two featureCounts generated from different studies
by
abedkurdi10
▴
190
What do you mean by gene lists?
Comment: Find potential important genes from bulk-RNA seq experiment
by
Michael
53k
You can use e.g. the WGCNA package for network analysis. In your case multiple samples this might mean multiple patients or a time series o…
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
•
0
Thank you so much for your responses.
@genomax , I've downloaded both of the databases you recommended. I attempted to combine them into …
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
by
Mensur Dlakic
★
24k
I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
Comment: Salmon index not progressing
by
camillab.
▴
130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴
180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
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