Increase sensitivity of SQUID

Kingsford-Group / squid

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

BSD 3-Clause "New" or "Revised" License

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Increase sensitivity of SQUID #15

Open readmanchiu opened 5 years ago

readmanchiu commented 5 years ago

Hi, I'm wonder if there is a parameter where you can increase the sensitivity of SQUID by lowering the number of reads supporting the fusion (the SCORE field in the bedpe file)? I wonder if there is a minimum cutoff set somewhere where you can change? I ask this because I clearly saw some chimeric alignment in my chimeric bam file but I don't see SQUID reporting the fusion.

Thanks, Readman Chiu

Congm12 commented 5 years ago

You can reduce the minimum edge weight parameter (-w), or increase the discordant edge weight multiplier (-r).

However, since SQUID currently only detect dominating TSVs, changing the two options may not guarantee to output the desired one. We are currently working on extending SQUID to detect heterogeneous TSVs. When that's done, the TSV detection will be more sensitive.