Rna-Seq Cancer Cell Line, Hg19 Or Cancer Cell Line Genome?

Question

[QVINTVS_FABIVS_MAXIMVS]

Just curious,

I never worked with cancer data before and I was wondering if it's not recommended to use the generic H.sapiens reference genome builds such as hg19

Should I build the .ebwt files using the genome from the specific cancer cell line, which in fact has a validated translocation?

I'm leaning towards the cancer cell line, but my reads are around 35bp in length after QC. So I'm guessing that it wouldn't really matter because of this?

Thanks a lot!

Answer 1

[Devon Ryan]

Does the translocation interrupt a transcription event? If not, the mapping will be approximately the same regardless.