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This has already been done, and the resulting files are at this URL: http://loving.corral.tacc.utexas.edu/bioiteam/ucsc_custom_tracks/, filename progeria_ctcf.vcf.gz. These are hg18 SNP calls from published Iyer Lab CTCF ChIP-seq data in Progeria cells. The VCF file was produce using Broad's GATK.

• Add custom tracks (be sure to pick assembly March 2006, NCBI36/hg18)
• Here is the track configuration line

  Code Block
  track type=vcfTabix name="progeria_ctcf_snp_calls" bigDataUrl="http://loving.corral.tacc.utexas.edu/bioiteam/ucsc_custom_tracks/progeria_ctcf.vcf.gz"

BAM data

BAM data can only be configured as a URL, not uploaded directly. Directions are found at http://genome.ucsc.edu/goldenPath/help/bam.html.

• The BAM file must be sorted and indexed using samtools. The .bam and .bai index file must reside in the same directory.

This has already been done, and the resulting files are at this URL: http://loving.corral.tacc.utexas.edu/bioiteam/ucsc_custom_tracks/, filename hela_totrna.sorted.bam. This is SE RNAseq data mapped directly to the human genome, hg19.

• Add custom tracks (be sure to pick assembly Feb 2009, NCBI37/hg19)
• Here is the track configuration line

  Code Block
  track type=bam name="hela_rnaseq" bigDataUrl="http://loving.corral.tacc.utexas.edu/bioiteam/ucsc_custom_tracks/hela_totrna.sorted.bam"

Here is another example, using paired end RNAseq data as processed using a tophat/cufflinks pipeline:

track type=bam name="rnaseq_bam" pairEndsByName=Y bigDataUrl="http://loving.corral.tacc.utexas.edu/bioiteam/ucsc_custom_tracks/accepted_hits.sorted.bam"

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