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Old 12-21-2010, 09:47 PM   #1
khb
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Location: Oslo

Join Date: Dec 2010
Posts: 15
Default Exons from UCSC (Refseq)

Hi
I've tried to get bed files for human exon, intron and promotor region. Used the http://genome.ucsc.edu/ Table browser and choosed track RefSeq genes.
Then I use intersectbed to see how many of my sequences have hits in promotor, exon and introns. But I have a problem in understanding the output of the refseq database. Here is some of the output from intersectbed.

chr1 908832 909142 MACS_peak_1 64.51 chr1 908706 908879 NM_032129_intron_11_0_chr1_908707_f 0 + 47
chr1 908832 909142 MACS_peak_1 64.51 chr1 909020 909212 NM_032129_intron_12_0_chr1_909021_f 0 + 122
chr1 908832 909142 MACS_peak_1 64.51 chr1 908390 908879 NM_001160184_intron_10_0_chr1_908391_f 0 + 47
chr1 908832 909142 MACS_peak_1 64.51 chr1 909020 909212 NM_001160184_intron_11_0_chr1_909021_f 0 + 122
chr1 967570 967836 MACS_peak_2 52.96 chr1 957842 970656 NM_198576_intron_1_0_chr1_957843_f 0 + 266
chr1 1198830 1199072 MACS_peak_4 77.66 chr1 1198766 1203112 NM_194458_intron_4_0_chr1_1198767_r 0 - 242
chr1 1198830 1199072 MACS_peak_4 77.66 chr1 1198766 1203241 NM_058167_intron_4_0_chr1_1198767_r 0 - 242

I want to count how many times introns have hits in my sequences, but I don't get what the parts of this name NM_032129_intron_11_0_chr1_908707_f stands for. What is the difference of the to first line in my output?

What about this output
chr1 1205861 1206212 MACS_peak_5 147.07 chr1 1203372 1209045 NM_194458_intron_5_0_chr1_1203373_r 0 - 351
chr1 1205861 1206212 MACS_peak_5 147.07 chr1 1203372 1209045 NM_058167_intron_5_0_chr1_1203373_r 0 - 351
chr1 1205861 1206212 MACS_peak_5 147.07 chr1 1203372 1209045 NM_194315_intron_6_0_chr1_1203373_r 0 - 351

is this just one hit or three different hits?

Thanks a lot
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