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dzhang32 / dasper

Detecting Aberrant Splicing Events from RNA-sequencing data
https://dzhang32.github.io/dasper/
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Error during junction loading #8

Closed biga94 closed 11 months ago

biga94 commented 11 months ago

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:

  1. SJ is a noncanonical motif and is only supported by < 3 unique mappings.
  2. SJ of length > 50000 and is only supported by < 2 unique mappings.
  3. SJ of length > 100000 and is only supported by < 3 unique mappings.
  4. SJ of length > 200000 and is only supported by < 4 unique mappings.
  5. SJ is a noncanonical motif and the maximum spliced alignment overhang is < 30.
  6. SJ is a canonical motif and the maximum spliced alignment overhang is < 12.

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

biga94 commented 11 months ago

I was able to solve by my own the problem. In my case, it was caused by some repeated rows under "chr", "start" and "end" columns in the SJ.out.tab files that altered the full join applied to the function. Both rows differ under the "strand" column, however I've decided to remove them. So, before proceed, remember to check unique rows especially when you deal with multiple junction files.

Best,

DB