Hi, guys:
I downloaded Illumina paired-end sequencing data (FASTQ Sanger format) into Galaxy, then performed "Map with Bowtie for Illumina" against hg19, "Filter SAM," "SAM-to-BAM," "Generate pileup," and "Filter pileup" with read quality ≥ 20, base coverage ≥ 3, and only report variants; "Convert genomic intervals to bed" and finally "BED-to-bigBed." The final interval format file is 94.0 Mb. I then selected the "display at UCSC main" option. In the browser I can see the "BED-to-bigBed on data #" line, and "region_######" indicators. If I select a "region_######" a single nucleotide is displayed, but it is Wild-Type. How do I see the variant nucleotides at this position? Thank you, Kevin Kevin Pawlik, PhD University of Alabama at Birmingham Biochemistry and Molecular Genetics Stem Cell Institute Shelby Bldg Rm 702 (office) | 776 (lab) 1825 University Blvd Birmingham, AL 35294 205-410-6861 [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
