Hello, I am a PhD student and during the analysis of sequencing data of miRNAs in the Galaxy project online tool an error occurred in the final stage of the analysis, when using the DESeq2 tool for the comparison of deregulated miRNAs between the two study conditions , the following error appeared:
Error in `levels
It looks like a problem with the DESeq2 object, a factor (conditions or levels) are duplicated. But without information about its construction, I cant help you. I recommend you to read: http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html to understand how to construct an adequate DESeq object, or, the galaxy project page ( https://help.galaxyproject.org/ ) for help.
But, in addition, I recommend you to use Bowtie (v1, not Bowtie2) to map sequencing reads from small-RNAseq, by default, it does not allow gaps in alignment, and therefore, the quantification of mature miRNAs is more accurate than Bowtie2 or Hisat2.
Best,
Check if any of your gene or the attributes which u have taken on the first column is getting repeated?
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA