Diverging results between STAR and BWA aligned inputs

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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Diverging results between STAR and BWA aligned inputs #33

Open yasin-uzun opened 1 year ago

yasin-uzun commented 1 year ago

Hi,

I am running squid with two types of inputs: 1) Samples aligned with STAR 2) Samples aligned with BWA

When using STAR output, I get less than 100 SV calls per sample. When I run with BWA output, I get several thousand SVs per sample. What is the source of this difference? Can you please give some information about this?