Comments (9)
It seems that when there is only one intron of length shorter or equal to 5bp annotated in one of the strands (in your case the only intron annotated for transcript ENSMUST00000051212.3
), an error arises in the arrow drawing due to an empty object. It should be fixed now.
from ggsashimi.
I think you should remove the commas for the region: 2:29619720-29740978
from ggsashimi.
nochr_gencode_full (copy).zip
i attached the gtf file also
$ ./sashimi-plot.py -b input_bam.tsv -g nochr_gencode_exon_transcript.gtf -c 2:29619720-29740978 -M 10 --base-size=20 --ann-height=4 --height=3 --width=18 -P palette.txt
Error in seq.default(start, max(start + 1, end - 4), by = 2425) :
'from' must be of length 1
Calls: rbind -> [ -> [.data.table -> seq -> seq.default
Execution halted
from ggsashimi.
Could you try only ./sashimi-plot.py -b input_bam.tsv -g nochr_gencode_exon_transcript.gtf -c 2:29619720-29740978
?, also with and w/o the annotation file to get some hint on the source of the problem. Can you reproduce our examples? In any case, could you provide some sample data to try to reproduce the error? Thanks!
from ggsashimi.
$ ./sashimi-plot.py -b input_bam.tsv -g nochr_gencode_exon_transcript.gtf -c 2:29619720-29740978
Error in seq.default(start, max(start + 1, end - 4), by = 2425) :
'from' must be of length 1
Calls: rbind -> [ -> [.data.table -> seq -> seq.default
Execution halted
and when i am trying without gtf it is working.
from ggsashimi.
So the problem could be the annotation. I see you use nochr_gencode_exon_transcript.gtf
. Could you try using the full annotation? Still, it would be really useful that you provide some example data in which we can reproduce the error. It can be just a (downsampled) bam file.
from ggsashimi.
Hi @archana433, did you manage to resolve the problem?
from ggsashimi.
yes, it is solved , Thank you
from ggsashimi.
I am getting this error again and also attaching the example data.
./sashimi-plot.py -b example1.bam -c 2:29619720-29740978 -g encode_mm10.transcript.exon.gtf
Error in seq.default(start, max(start + 1, end - 4), by = 2425) :
'from' must be of length 1
Calls: rbind -> [ -> [.data.table -> seq -> seq.default
Execution halted
gencode_mm10.transcript.exon.zip
from ggsashimi.
Related Issues (20)
- Error in R HOT 2
- Error running docker latest docker image (v.1.1.0) HOT 2
- error regarding intersect_introns HOT 17
- IndexError: list index out of range HOT 3
- C stack usage error HOT 3
- Error in FUN(X[[i]], ...) : object 'V1' not found HOT 2
- Individual exon junction cut-off
- Duplicate coverage output HOT 3
- Program hangs / freezes HOT 2
- Help with example HOT 1
- Output PDF HOT 2
- So many junctions and intron-like gaps HOT 2
- Colors not working HOT 2
- Junctions not being plotted or generated when running HOT 1
- Executing ggsashimi with singularity HOT 4
- How assign color if I am interested only in one sample HOT 1
- ggsashimi can easy read from remote BAMs if allowed to do it
- Duplicate arc appears for each junction using example_run.sh HOT 1
- ERROR: No available bam files. HOT 1
- Labels of sashimi plot 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 ggsashimi.