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WormLabCaltech / alaska

Automated and friendly RNA-seq analysis (deprecated)
http://alaska.caltech.edu
MIT License
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PRJEB28388 and paired end errors #41

Open raymond91125 opened 4 years ago

raymond91125 commented 4 years ago

Submitted from the feedback form on the WormBase website.

We are using Alaska software to analyse our RNAseq data. We have two bugs to report:

  1. Two of the C. elegans reference genomes give errors. When using the ref genome PRJEB28388, our analysis at failed at step 3 (differential expression analysis. When using ref genome PRJNA275000, analysis failed at step 2 (alignment and quantification). Our analysis was successful when using ref genome PRJNA13758.
  2. When inputting our reads as single end, our analysis was successful. When inputting our reads (in the same folders) as paired end, Alaska asked us to select our read pairs in the sample-specific metadata form. Instead of giving us the option to pair for example 'sample_1_read_1' with 'sample_1_read_2' (which showed up on the form), it only gave us the option to pair with the identical file i.e. 'sample_1_read_1' with 'sample_1_read_1'. In the meantime, we are analyzing our data as single reads, but would appreciate some help with inputting up our data as paired reads. Thank you for any help you can provide!