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323

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Ori-Ter normalization [Chip-seq]

next-gen chip-seq normalize written 7 months ago by anu014 • 150

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393

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Normalizing fails due to incorrect column count

vcf normalize written 12 months ago by andrewl • 10

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870

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Compare ChIP-seq data from various experiments

visualisation chip-seq normalize written 20 months ago by bharath.mh24 • 0

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669

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Normalize with Scale to method

R limma normalize written 23 months ago by mad.cultist • 0

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1.3k

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Chip-seq common control for two treatments

chip-seq normalize written 3.6 years ago by cg • 10 • updated 3.6 years ago by Ying W • 3.8k

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Recent Replies

C: Could you help me set up a VCF filter? by WouterDeCoster ♦ 29k
I'd first like to see if we can do some "manual" filtering. That would be quicker. How many genes...
C: Could you help me set up a VCF filter? by flutabex • 0
That's right, also on predicted impact. My computer is a 2 year old Thinkpad, Intel i7-5600U CPU ...
C: Could you help me set up a VCF filter? by WouterDeCoster ♦ 29k
I'm not sure how powerful your computer is, but alignment isn't too difficult. But let's take a ...
C: Issue with reverting bam file back to fastq files by genomax ♦ 49k
It would be helpful to edit the original question and add this information there. This thread has...
C: Could you help me set up a VCF filter? by flutabex • 0
Ah, thanks for checking that out, saved me a lot of time. I didn't do the alignment, only have th...
C: Issue with reverting bam file back to fastq files by williamsbrian5064 • 80
Thanks for doing that finswimmer! I apologize for that. I didn't realize that everyone got a noti...
C: Does FDR value change based Fold change cutoff? by Kevin Blighe ♦ 21k
To gain a full appreciation of what's going on, you should be outputting, in addition, things lik...
C: Could you help me set up a VCF filter? by WouterDeCoster ♦ 29k
I'm sorry, I just read this in the manual: > GEMINI solely supports human genetic variation m...
C: Could you help me set up a VCF filter? by WouterDeCoster ♦ 29k
I assume you haven't done the alignment yourself? If so, you could convert the reads back to fast...
C: Could you help me set up a VCF filter? by flutabex • 0
Thank you, I will have a look.
C: Could you help me set up a VCF filter? by WouterDeCoster ♦ 29k
I haven't used it myself, but perhaps gemini is a solution http://gemini.readthedocs.io/en/latest/
C: bcl2fastq report the whole sequences without trimming index and adaptor by genomax ♦ 49k
Ok. Sounds like your issue is on experimental side rather than the demultiplexing. Check to see i...

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