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Home Page: https://dzhang32.github.io/dasper/
Detecting Aberrant Splicing Events from RNA-sequencing data
Home Page: https://dzhang32.github.io/dasper/
Hi,
Thanks for the awesome tool!
I'm trying to plot coverage and coverage plotting functions supports a single case sample at a time. Can you please suggest on how I could plot mean coverage from multiple bigwigs?
Hi David,
I tried fixing lcolladotor/derfinder#42 and updating the GHA workflow to use biocthis 1.3.6 but I ran into:
$ git remote -v
origin [email protected]:dzhang32/dasper.git (fetch)
origin [email protected]:dzhang32/dasper.git (push)
13:15 dasper $ git push origin
ERROR: Permission to dzhang32/dasper.git denied to lcolladotor.
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
Best,
Leo
Hey there,
I'm trying to load my SJ.out.tab files produced using DRAGEN RNA Pipeline. The file produced by this pipeline is pre-filtered, using these rules declared on Illumina support:
However, as I try to load my files, here comes the error:
Error in .junction_merge(junctions_all, junctions) : No strands should be left as NA after processing
Do you know how to deal with it?
Best,
DB
Hello
Thanks for developing dasper.
I have an issue with coverage_norm
function, where it fails with megadepth.
Essentially, the quotes around the path of the input bigwig file are stripped, so space characters in that path are now interpreted as breaks in the command, and it fails.
Although I submit my list of bigwig files using properly formed paths (with quotes), these quotes are stripped from the megadepth command that is run.
There are a few space characters in the path. My working directory is on OneDrive with a path I cannot change. I have no issues with running other R commands at that location, as a matter of fact the said bigwig files are made with GenomicAlignemnts::coverage and saved there with rtracklayer::export.bw.
I should also mention that I took the megadepth command echoed in the error message, I added the quotes that had been stripped, and I ran that in a command prompt window and it ran fine, yielding a temp file with name ending in _coverage.annotation.tsv
So my questions are:
-what would be the fix to avoid the stripping of the quotes? Where is the line of code that forms this command?
-I don't mind issuing the megadepth commands separately, but how would I go about picking up from there afterwards?
Thanks in advance for your help.
Alex
Could you please help me with this? Thank you!
Best,
Salwa.
Hello,
I tried the following to install dasper but got errors:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("dasper")
which gave me this error:
Warning message:
package ‘dasper’ is not available (for R version 4.0.2)
Then I tried
BiocManager::install("dzhang32/dasper")
and got:
ERROR: dependency ‘megadepth’ is not available for package ‘dasper’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dasper’
Error: Failed to install 'dasper' from GitHub:
(converted from warning) installation of package ‘/var/folders/6b/fk6yw91n0gn9r5sr99yc88x5_r9zrk/T//Rtmp2WW3yy/file1165c7f39b482/dasper_1.1.6.tar.gz’ had non-zero exit status
I tried to install megadepth but got error that it is not available for R 4.0.2 BiocManager::install("megadepth")
Warning message:
package ‘megadepth’ is not available (for R version 4.0.2)
Not sure what to try next. Thank you
When running outlier_detect, I encountered this error
Error: BiocParallel errors
1 remote errors, element index: 1
1 unevaluated and other errors
first remote error:
Error in py_module_import(module, convert = convert): ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /home/chualec/.cache/R/basilisk/1.10.2/dasper/1.7.0/env_sklearn/lib/python3.8/site-packages/scipy/spatial/_ckdtree.cpython-38-x86_64-linux-gnu.so)
I tried a few things to solve it, including updating the conda environment and installing gcc, but it didn't help.
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