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Recent Replies
Answer: ChIP-Seq with one poor replicate, one good
by
Ian
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You could try MANORM ([https://github.com/shao-lab/MAnorm][1]) which compares two samples.
Did you try DiffBind using TRT (1 sample) vs …
Comment: How can a graduate student start offering bioinformatics pipeline development as
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Joe
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I'm not sure how it works in other countries, but in the UK at least it would be quite unusual for a freelancer to be 'employed' on a resea…
Comment: intersect question of H3k4me3, H3k27Ac, H3k27me3, calculating the consensus
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theodore
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I ended up shrinking with removing something like 500 bps (with bedtools slop) of the H3k27me3 peaks and manually remove some that were not…
Comment: RNASeq QC and STAR results confused
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My bet would be that, since it is total RNA sample, it might not have been rRNA depleted. That will certainly result in the numbers you men…
Comment: Germline and somatic mutations TCGA (GDC Data Portal)
by
Charlotte Stubbe
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Dear Kevin
We have access through dbGaP, so that is no problem.
**somatic** With processed data, do you suggest then using PASS from Mut…
Comment: RNASeq QC and STAR results confused
by
1769mkc
★
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please show the plots or data table, may be you can share your multiqc report.
Comment: Batch Effect
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ATpoint
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I do not know EBSeq, but generally, any testing framework suffers when n is low and data are noisy. I use limma with the weighting a lot si…
Comment: How can a graduate student start offering bioinformatics pipeline development as
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Yes, I have a github going of projects and analyses I did. The OP was more to do something productive over winter break, but there are plen…
Comment: How can a graduate student start offering bioinformatics pipeline development as
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Istvan Albert
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I think the most important thing is to have a visible portfolio - like a github repository that you can use to convince people that you can…
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> I want to perform directed RNA-seq Nanopore-derived data
Can you confirm that you are looking to do direct RNA sequencing that is "adapt…
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Hi Istvan,
Thank you for the realistic answer. I redid analyses from interesting papers by using both the workflows in your book, the Bio…
Answer: How can a graduate student start offering bioinformatics pipeline development as
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Istvan Albert
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Don't freelance - it does not scale and you run the risk of selecting for mismanaged projects. What serious person would hire a freelancer …
Comment: Batch Effect
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Umair
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Thank you @atpoint for the detailed advice. I was considering applying EBSeq for DEG. Now, I think I should rely on limma framework. I am w…
Comment: Interpretation of logFC in limma-voom contrasts
by
donan
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Thank you very much, this was really helpful. And of course, I'll try to get more information about the data as soon as possible.
Comment: Interpretation of logFC in limma-voom contrasts
by
donan
•
0
Thank you very much for the clarification and for the normalization recommendation.
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