search

MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
MIT License
136 stars 28 forks source link

Tandem_contraction empty when long unqie_anchor_length choosen #5

Closed BenjaminSchwessinger closed 7 years ago

BenjaminSchwessinger commented 7 years ago

The Tandem_contraction is empty when I chose unquie_anchor_length 50kbp compared to 10kbp.

Any reason?

http://qb.cshl.edu/assemblytics/analysis.php?code=SUIBTG2OcqVoxxqb6eKK http://qb.cshl.edu/assemblytics/analysis.php?code=vDHlfEIeWnTDLyhn3eVn

MariaNattestad commented 7 years ago

The 4 tandem contractions you had at 10kbp were likely in alignments that were anchored in less than 50kbp unique sequence, so when you increased the level to 50kbp those alignments got filtered out and the variants in them were no longer called.

BenjaminSchwessinger commented 7 years ago

Thanks this makes sense.