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Why most super enhancers identified by ROSE were located on promoter regions? How can I remove them?
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Recent Replies
Answer: p-values in GTEx
by
Shicheng Guo
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8.9k
QTL Mapping using FastQTL
cis-eQTL and cis-sQTL mapping was performed using FastQTL (Ongen et al., Bioinformatics, 2016 ), using the covar…
Comment: How to apply lapply function and loop function at the same time
by
Phylicia
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Thanks a lot！
Comment: High duplicate BUSCOs after annotation but not assembly
by
jaredbernard
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Thanks! I'm trying it now.
Answer: High duplicate BUSCOs after annotation but not assembly
by
BioinformaticBird
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This is not a direct answer, but maybe you can verify your BUSCO results with [MOSGA][1], uploading both sequences. Generally, the annotati…
Comment: High duplicate BUSCOs after annotation but not assembly
by
jaredbernard
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Thanks, Juke. I think you're right. I've been using JBrowse to visualize, so I'll take another look. Yes, I'm concerned that the duplicates…
Comment: High duplicate BUSCOs after annotation but not assembly
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Thanks for the feedback, Michael. I used BUSCO on the exons from Maker's final annotation, set on transcriptome mode and selecting the line…
Answer: Annotation pipelines in 2018
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BioinformaticBird
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In the hope of keeping this thread alive, I suggest the most accessible eukaryotic genome annotation pipeline/framework: MOSGA.
[https://mo…
Answer: How to annotate eukaryotic genome
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The easiest way is to use MOSGA, a freely modern and easy-to-use eukaryotic genome annotation tool. It runs online (or you can set it up ma…
Comment: A question regarding the differential coverage binning process in a metagenomic
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Rui
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I see, thank you!
Comment: mutation found in RNA seq data and not in DNA data
by
Mensur Dlakic
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A mutation in coding DNA (and subsequently captured by RNA-seq) could lead to protein mutation with a good probability. Mutations in the th…
Comment: mutation found in RNA seq data and not in DNA data
by
Mensur Dlakic
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That would support a sequencing error as a likely cause of mutation, although it is possible that there is a small fraction of mutations in…
Comment: Cytoscape : problem importing networks from String databases
by
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Thank you very much for your reply ... very reassuring! Shall wait and try again.
All the best
Comment: mutation found in RNA seq data and not in DNA data
by
pingu77
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Also a mutation in both data (DNA and RNAseq) is unlikely to lead to mutations at a protein level, right? I guess the most interesting case…
Comment: mutation found in RNA seq data and not in DNA data
by
pingu77
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Hi GenoMax, thanks for your question! it is low, I have in total 20 reads and the mutation is just in 2 of them.
Comment: Cytoscape : problem importing networks from String databases
by
Mensur Dlakic
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I don't think it is necessarily anything you did wrong. I see the same thing as you and STRING seems not to be available. I am guessing it …
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