leekgroup / recount-contributions Goto Github PK
View Code? Open in Web Editor NEWContribute your human Illumina RNA-seq data to recount2
Home Page: https://jhubiostatistics.shinyapps.io/recount/
License: MIT License
Contribute your human Illumina RNA-seq data to recount2
Home Page: https://jhubiostatistics.shinyapps.io/recount/
License: MIT License
To whom, it may concern.
I would like to run the same pipeline used to generate Recount2 in my dataset.
To check if the rail-RNA pipe worked correctly I ran it on a small project uploaded in Recount2 (SRP047399)
Rail-RNA was run using this command:
rail-rna go local -x dir_bowtie_hg38 dir_bowtie2_hg38 -m manifest_file --log dir_log_file -d tsv,bw,jx -f --scratch temp_folder_dir
based on Bowtie and Bowtie2 indexes for the reference genome hg38. Downloaded from:
I genome Illumina:
I used the following data to run the R scripts after the rail-RNA pipeline.
However when I match the gene counts or exon counts that I obtained against those uploaded in Recount2 I found some differences. In some cases, these differences resulted in more than 100.000 read counts
Moreover, I get this error when I run the prep_merge.R script
oo <- findOverlaps(jx_gr, introns_unique, type = 'equal')
stopifnot(length(unique(queryHits(oo))) == length(oo))
Can this be due to the use of wrong annotations?
I read that the tool is deterministic, I expected to obtain the same results. I check the number of reads in input and they are the same. However, the number of mapped reads is different
Do you have any idea why this happens?
Considering that I would like to compare my samples with the data in Recount. Please, can you confirm that the pipeline and the reference and the annotation files are correct?
Thank you.
Best Regards,
Gianluca
Please find below an example for one of the sample.
SRR1583592_my results | SRR1583592_recount2 | |
---|---|---|
4398 | 1345 | |
108156 | 108153 | |
15685 | 15685 | |
1 | 0 | |
47805 | 115970 | |
195 | 195 |
I've been trying to follow the instructions for preparing my data after running Rail-RNA and am having problems with the amount of dependencies these additional tools need and getting them to run. Some do not look to be maintained.
Release of a docker container would greatly assist this if it is possible.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.