Comments (2)
Chromosome names in two files (tss_enrich
and chrsz
) don't match.
Your chrsz file looks like.
$ cat rn6_masked.chrom.sizes.txt | head
1 282763074
2 266435125
3 177699992
4 184226339
5 173707219
6 147991367
7 145729302
8 133307652
9 122095297
10 112626471
Your tss file.
$ zcat tss.rn6.bed.gz | head
chr1 100037072 100037073 ENSRNOG00000048901 0 +
chr1 100047235 100047236 ENSRNOG00000045980 0 +
chr1 100059967 100059968 ENSRNOG00000032857 0 +
chr1 100086520 100086521 ENSRNOG00000032857 0 +
chr1 100131449 100131450 ENSRNOG00000032857 0 +
chr1 100131562 100131563 ENSRNOG00000032857 0 +
chr1 100161872 100161873 ENSRNOG00000033414 0 +
chr1 100164400 100164401 ENSRNOG00000054979 0 +
chr1 100189515 100189516 ENSRNOG00000033805 0 +
chr1 100199057 100199058 ENSRNOG00000032857 0 +
from atac-seq-pipeline.
Are new versions tested with sample data before being committed? I've been submitting bugs related to non-conventional chromosome names for 6 weeks now and have not been able to get a sample to run to completion.
from atac-seq-pipeline.
Related Issues (20)
- Finished parsing without consuming all tokens HOT 1
- How are mitochondrial reads aligned? HOT 1
- How are DNAse-seq data processed with this pipeline?
- Reuse the same files in case of error.
- Help with running the pipeline HOT 1
- Unable to run the pipeline. invalid jar file error HOT 3
- 6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running
- More than 10 replicates HOT 3
- Encode-atac-seq-pipeline environment can't be found?
- [Question]: Do reads need to be deduped before FRiP calculation HOT 6
- Invalid MEMLIMIT unit value with LSF jobs on Linux
- two replicates and the combined have different signal
- --read-len selection
- Memory Saving: too many large files?
- The pipeline stalled at "chip.read_genome_tsv" for local backend HOT 2
- Differences in qc when validating installation HOT 3
- Failed on fastqs having identical filename but different path HOT 3
- Confirming that separate conditions/treatments should be analyzed by separate pipelines HOT 2
- Don't need to trim adapters
- Add --ntasks-per-node or --exclusive option for your multi-process jobs.
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 atac-seq-pipeline.