Genomic mapping

Galaxy thinks gd7 fastq all have low quality scores (1 to 4 on a scale of -5 to 40).

Mapping .gff gd7 reads to browser to check quality.  Looks good on UCSC browser, except that squish display doesn’t work.

Taking +/- 100 bp of promoter to ID paused promoters. Map to genome (dm2), use count to convert to scores per gene.  Align to tiling data.

Take c1>1000 (raw reads aligned to promoter) and c3-c4 > 5 (raw tiling array 5 greater in toll10b than gd7)

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