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Does anyone know where I can download the hg19 exon and intron coordinates of a particular gene (SPRED1)? Thanks.
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Try UCSC table browser : http://genome.ucsc.edu/cgi-bin/hgTables
direct link :
Make sure it's set to UCSC hg19 refGene
Use these cooordinates : chr15:38,518,952-38,675,550
(i.e. the location of the SPRED1 gene on hg19 )
output ...
#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames
879 NM_152594 chr15 + 38545051 38649450 38545386 38643865 7 38545051,38591573,38614441,38616963,38631937,38641622,38643214, 38545418,38591748,38614610,38617010,38632096,38641724,38649450, 0 SPRED1 cmpl cmpl 0,2,0,1,0,0,0,
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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