1. Download Human Genome Reference from NCBI using NC_0000* at the Search functionality of CLC; download the top 24 sequences to a new folder under CLC_data folder; change the name of each file to chr1, chr2 et al. -- they are all .clc files in CLC now.
2. Annotate_with_GTF: download the GTF file of human genome from the UCSC genome browser (follow the manual and choose ALL_SNP_132); save it under the folder of "humansnps(ALL_SNP_132)_1010" (unzip it and give a file extension gtf to it). Then this gtf file will match 24 chromosomes above as annotating.
Simply follow the manual; the annotation will be added to the original 24 chromosomes' clc files -- they are ready for mapping reads to reference.
3. Map reads to reference: follow the manual "Genomics_Gateway_User_Manual"; select "Homo sapiens tracks"; uncheck "Add tracks to existing track set".
It takes 24 hours.
4. A new track "Homo sapiens reads track" will be saved under the same folder.
5. SNP detection: follow the default setting except min coverage set to be 100.
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