Comments (2)
Hey,
the cropping is probably only done in the error message, I can hardly imagine STAR doing something as substantial as this without giving a warning at least.
For the length inequality problem there are some related issues - maybe one of them applies to your data:
- Real length inequality
- Potential invisible characters, could also be related to windows
- Messed-up file formatting, potentially related to trimming
- Something related to nanopore sequencing
- Multi-line FastQs
- GZ corruption
- Inconsistencies in paired-end usage
However, this problem is most likely not related to our pipeline and should thus be checked by running STAR on your data without the pipeline
from circrna.
Closing this for now, feel free to re-open if the problems persist
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Related Issues (20)
- Process exceeded running time limit (16h) HOT 2
- Add strandedness column to samplesheet HOT 1
- Problem with star 2nd pass, Process exceeded running time limit - CIRCexplorer2 HOT 4
- ERROR ~ Argument of `file` function cannot be null HOT 5
- Fatal INPUT FILE error, no valid exon lines in the GTF file: genes.gtf when using --genome GRCh38 HOT 1
- Deprecated mapsplice docker image: quay.io/biocontainers/mapsplice:2.2.1--py27h07887db_0 HOT 1
- Implement JCcirc
- Implement CIRI-full
- Implement circRNAfull
- Implement psirc for isoform detection
- Implement miRNA sponging analysis
- Implement circRNA database search functionalities
- Implement circbase
- Implement circatlas
- Implement circbank
- Implement circRNADisease
- Implement polyA-Benchmarking
- Decide how to proceed with the differential expression subworkflow
- Deprecate the `module` parameter
- Add `psirc quant` output to MulitQC via `kallisto` module
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from circrna.