Skip to content

Updates and bugfixes
Compare
Choose a tag to compare
@nedialkova-lab nedialkova-lab released this 09 Aug 13:31
· 57 commits to master since this release
v1.3.6
899fad8

Updates

  • Added Biopython SeqIO functionality for Stockholm file parsing - see ssAlign.py. This removes all necessity to filter tRNAs with poor secondary structure alignment from the input reference. This was being done before for some genes in hg38 and gorGor4 references to prevent multi-line alignments in stk files.
  • Updated gorGor4 and hg38 references. No genes are filtered out from full set (except for one gene in gorGor4, see README
  • Added C. elegans reference and updates to A. thaliana reference
  • Misincorporation signature required to find new modification was previously set at no more then 95% misincorporation of one nucleotide (to distinguish from SNPs or inosine). This is now 97% which we find more permissive to detect important modified sites that are verified as modifications.

Bugfixes

  • DESeq2 dot plot axis labels: remove "log10" as the values are not log scaled but only the scale of the axis.
  • Installation instructions updated to include the installation and use of condaforge/mambaforge offering better speed and environment resolution and dependency handling.
Assets 2
Loading