Comments (11)
@chlazaris it should be a call that involves the key nf-core devs who have been working on this, for example @JoseEspinosa or @drpatelh . Maybe this is a conversation that could happen on the nf-core Slack channel initially to organize something?
from chipseq.
@cjfields this is a good idea. Please, feel free to start the discussion there but include @nservant in addition to @JoseEspinosa and @drpatelh, as he was the one who developed the version with spike-in normalization and IDR. Thank you!
from chipseq.
Hi all, just commenting in support of adding spike-in normalization similar to nf-core/cutandrun. It's an invaluable technique for ChIP-seq
from chipseq.
Hi guys, sorry for the delay. Happy to further discuss if needed
from chipseq.
This would be great to add as I've seen spike-ins being used in a few ChIP-Seq projects. I believe the only place spike-in normalization is included is with the bigWig file however, @EmanuelSoda is that your experience as well?
from chipseq.
Hi,
As far as I know it is also possible to normalize in some way the bam files in order to obtain a more reliable quantification afterwards. But I am not sure how.
from chipseq.
Spike-in normalization would be a very useful addition. @nservant has written a Nextflow pipeline which provides this feature in addition to others (https://github.com/bioinfo-pf-curie/ChIP-seq). I am testing it at the moment but it would be really useful to have the official nf-core ChIP-seq pipeline support this option.
from chipseq.
@chlazaris would it make sense to combine efforts here? It seems like there is considerable overlap, but the workflow from @nservant seems to tick a few more requests like spike-in norm and IDR, and nf-core has other options the above workflow is missing.
from chipseq.
Hello @cjfields, this is what I see too. We should probably have a Zoom call to see what the best options are. My time zone is EDT. What is the best way to reach you? Thanks
from chipseq.
Just a small note, there are different methods for spike-in norm that should be considered, for example:
https://github.com/hbctraining/Intro-to-ChIPseq-flipped/blob/main/lessons/spikeIn_normalization.md
from chipseq.
Hello @nservant and everyone else interested in spike-in normalization. Since, you have already worked on a version of the ChIP-seq pipeline with spike-ins @nservant, I am wondering what could be done to incorporate the spike-in normalization feature to the official nf-core pipeline, as the broader community would benefit a lot from this. There is an active thread on the nf-core Slack workspace. @cjfields started it and can be easily found by searching for "spike" on the #chipseq
channel. Thank you and I will be happy to discuss further.
from chipseq.
Related Issues (20)
- Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1) HOT 3
- mergeBed ERROR: Requested column 10, but database file - only has fields 1 - 9. HOT 18
- Normalisation of bigwig files
- package or namespace load failed for ‘UpSetR’ HOT 3
- No Space left on device error HOT 3
- Make subworkflows & modules available for nf-core tools HOT 1
- Default values for p-value and FDR HOT 2
- Get rid of checkIfExists for params paths HOT 1
- minor "samplesheet_pe.csv" format issue HOT 1
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model! HOT 2
- Error with NextSeq trimming HOT 2
- Error running the pipline test in the BWA index step HOT 2
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3 HOT 1
- There are multiple files for each of the following file names
- Can't run if there is no control HOT 2
- Improve website on parameters section Alignment Options for argument --save_unaligned HOT 1
- IDR analysis HOT 2
- Remove lib folder to get ready for v2.13.1 template merge HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from chipseq.