Hi there, I was given the following RNASeq paired-end data and looking for ways to visualize it on the genome browser. The file is a processed SOAP aligned, paired-end, Illumina, mapped to hg19.
The file contains the following columns (tab delimited): ID seqOne seqTwo chromosome oneStarts oneStops twoStarts twoStops Looking at this example of a paired-end junction: HWUSI-EAS474_21_30E9BAAXX:2:1:766:164 is the ID GCACAGCAGAAGTGTTTTTCTTTTTTTAATGAACAA is the left end GTCCCATGTTGACAATTTGTATGGTTTACTTTTTCA is the right end chr12 is the chromosome 14954338,14956285, are the starts for the left end, which aligns to a junction 14954362,14956297, stops for the left end 14954311, right end start 14954346, right end stop Here is a snapshot of a few lines from the actual file: GA2:1:1:32:1827#0 AAATTAGACAACTGATGTCATGCTGTCTTGGTCTCC GTGGAAACAAGTAATGGAACCAACGCCCTGTGTGTA chr11 16779120, 16779155, 16779542, 16779577, GA2:1:1:34:1274#0 TGGTGACCTTCAAGGAATCTTTGAGGGCCTGGAGCT TCCAGGAGCAGCTCCAGGCCCTCAAAGAGTCCTTGA chr11 71726406, 71726441, 71726415, 71726450, (and a junction read) : GA2:1:1:105:706#0 TGGCAGTGCAAATATCCAAGAAGAGGAAGTTTGTCG CCTGGTTGGTGTAACTCGCACCTCAACTCCAGAGTA chr11 75110593,75111737, 75110621,75111745, 75111807, 75111842, Would really appreciate your advice on how to prepare this file to visualize it the UCSC GB especially with the multiple coordinates for the junction tags. I was advised that BED file might work here however not sure how to set-up the files based on the instructions that was provided in FAQ Data File Formats Thanking you in advance. Cheers, Rathi -- Rathi D. Thiagarajan PhD Candidate GenitoUrinary Development Molecular Anatomy Project(GUDMAP) Queensland Centre for Medical Genomics Institute for Molecular Bioscience University of Queensland, St. Lucia, QLD 4072 AUSTRALIA T: +61 7 3346 2609 F: +61 7 3346 2101 E: [email protected] W: http://www.qcmg.org _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
