With the advice of several members of the SEQanswers forum and a lot of reading, I was able to go from Illumina ChIP-seq reads to viewing alignments in the UCSC Genome Browser - Thanks! Also, a huge thanks to the UCSC team for a great resource.
I thought the next step would be easy (I can hear the chuckling now): I want to analyze these data with the UCSC Table Browser to determine the number of reads that align to different features (e.g. CpG islands). My custom tracks are in BAM format and I keep getting errors when I try to add them to the Table Browser (e.g. # No results returned from query).
Then I converted my BAM files to BED files, but the upload to UCSC times out when I use the following URL format (without the "-" at the beginning):
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=susScr2&position=chr7&hgt.customText=http://mysite.edu/MyReads.bed
Now I am about to try to convert my BED files to BigBED format. Before I do this, is there an easier way to just view my BAM files in the Table Browser that I am just not seeing (or more likely, a mistake I am making)?
Many thanks in advance,
jjw
I thought the next step would be easy (I can hear the chuckling now): I want to analyze these data with the UCSC Table Browser to determine the number of reads that align to different features (e.g. CpG islands). My custom tracks are in BAM format and I keep getting errors when I try to add them to the Table Browser (e.g. # No results returned from query).
Then I converted my BAM files to BED files, but the upload to UCSC times out when I use the following URL format (without the "-" at the beginning):
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=susScr2&position=chr7&hgt.customText=http://mysite.edu/MyReads.bed
Now I am about to try to convert my BED files to BigBED format. Before I do this, is there an easier way to just view my BAM files in the Table Browser that I am just not seeing (or more likely, a mistake I am making)?
Many thanks in advance,
jjw
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