Galaxy |

ctat_lncrna (version 1.0.0)

Bed File::

Reconstructed transcripts (ex. from StringTie or Trinity)

Min overlap:

Remove any transcript that overlap annotated coding gene greater than min_overlap

Min cluster:

Minimum size of duplication clusters to remove

Min exonic identity to filter out transcript that aligns to orthologous coding gene:

default is set by learning coding alignment distribution from data

Min match:

Minimum match parameter for liftover

Pad:

No. of basepairs to search up- and down-stream when lifting over lnc to ortholog

Gap open penalty to pass to lastz:

Decreasing this parameter will increase sensitivity of orthology search

Gap extend penalty to pass to lastz:

Decreasing this parameter will increase sensitivity of orthology search.

Choose annotation::

Select annotation

slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution.

To learn more about slncky visit their website .