Comments (9)
The order of groups in samples.groups.csv
should define the comparisons. If there are two groups, the first one is the reference.
from sns.
That is excellent
Thank you
from sns.
Hi Igor, I am using your pipeline and find it super helpful! Thank you so much! I have successfully run the rna-star pipeline and wanted to run the rna-star-groups-dge. Somehow I am however having issues for the pipeline to accept the file "samples.groups.csv". Even though I have renamed the groups and replaced it in the same folder with the same name, I keep getting the error message of "ExitCode 1" (via email). In the terminal I get this error message: CMD: sbatch --time=10:00:00 --nodes=1 --ntasks=1 --cpus-per-task=5 --mem=50G --job-name=sns.rna-star-groups-dge --mail-user=[email protected] --mail-type=FAIL,REQUEUE --export=NONE --wrap='bash /gpfs/data/jhubbardlab/sns/routes/rna-star-groups-dge.sh /gpfs/data/jhubbardlab'
Submitted batch job 48128185
How do I write the file "samples.groups.csv" properly into the repository, or is there anything else that I do not do correctly and need to adjust?
Thanks so much for your help!
from sns.
Did you check the full log file?
In the logs-sbatch
directory, there is a log file for every sbatch job. You can view it in the terminal with cat logs-sbatch/slurm-[jobid].out
or download it and open it with any text editor. If you are not sure what to look for, you can copy and paste the contents or attach the whole file here. Generally, the last few lines (right before the job ends) are the most relevant ones for troubleshooting the error.
from sns.
Thanks for the fast reply Igor! There was no logs-sbatch directory prior to running the command you sent. And after the command it says "No such file or directory". After your command there is a folder with logs-sbatch, but its empty.
from sns.
I found the file you were referring to, even though it was not in the expected folder. I think the issue is that I do not have replicates, which are required since version v1.22. Is there any chance I could use an older version?
from sns.
It is not possible to estimate variability of a gene without replicates, so any statistics would not be particularly meaningful.
If you don't have replicates, you can use DESeq2 1.18. It's part of Bioconductor 3.6, which requires R 3.4. Many other packages would need to be downgraded as well. As you may imagine, that would require a lot of troubleshooting.
Alternatively, you can assign all samples to a single group and DESeq2 will generate a table of normalized counts. You can then calculate a fold changes based on that.
from sns.
Hi Igor, thanks for coming back to me so quickly! I have pooled all my worm replicates into one sample. I guess I should not have done that.
I am now left with three mutants, and no replicates. so if I were to assign them a single group, I would not be able to make comparisons?
Alternatively, is there a way of splitting the data into three batches now? I guess that is not the proper way to do, but I am trying to avoid having to run the experiment again.
Thank you so much for your help in figuring this out!
from sns.
I assume you mean you pooled them before library prep and sequencing. It is too late in that case.
You could still calculate fold changes and look at the top genes. You just can't do any proper stats.
from sns.
Related Issues (14)
- Route for just FastqScreen? HOT 1
- question HOT 1
- fastq HOT 2
- Question Regarding PCA plot HOT 1
- Problem with differential expression analysis HOT 14
- WES 'rebuild' route, or other per-section pipeline running HOT 1
- qsub delay is too slow HOT 1
- pipeline does not work if analysis directory is moved HOT 6
- errors in wes-pairs-cnv pipeline HOT 5
- access to genome dir? HOT 8
- newbie HOT 12
- exitcode1 by slurm HOT 16
- ERROR: the value for setting EXP-TARGETS-BED must be specified logs-sbatch/slurm-18641451.out: qc-target-reads-gatk.sh ERROR: BED DOES NOT EXIST HOT 14
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 sns.