search

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
40 stars 22 forks source link

Example output file? #20

Closed stianlagstad closed 4 years ago

stianlagstad commented 4 years ago

Hi,

I would like to know if the output data that SQUID produces can be used with https://github.com/stianlagstad/chimeraviz. Do you have any example output files that you can share?

Thank you!

Congm12 commented 4 years ago

Hi,

Please see the following example of output file in the attachment of an HCC1954 sample using GRCh37 genome. The meaning of each column is in the Output Specification section.

hcc1954_sv.txt

stianlagstad commented 4 years ago

Thank you very much. Is it alright if I include that file in the chimeraviz package, as example data? If ok with you, I'll add that in this PR: https://github.com/stianlagstad/chimeraviz/pull/79

Congm12 commented 4 years ago

That's totally fine.

stianlagstad commented 4 years ago

Thanks again!