Hi, guys, which one should I use to build index? Is HG18 more complete than HG19?
-
-
Depends on your goal. Typically I would recommend using the newest genome version but you may have a situation that requires hg18, however, almost all applications/resources have now moved to hGRC37/hg19. The one issue seeing your other post is some versions of hg19 are to big for the BWA index step (see my intro post for description and options I found) also are you converting reads from illumina format to sanger format fastq? If not do so before you align. -
What is the difference between Illumina FASTQ format and Sanger format? I thought the only difference is offset.Comment
-
If you mean the Phred like quality score values, then yes you are correct the seemingly relevant issue is the scale/offset +33 versus +64 difference. But you need to convert to the sanger scale values or your variant calling will not work correctly.Comment
-
Thanks for the answers.
Lets say after I convert, if I want to use the -q option what is the best value to choose?Comment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment