Hello everyone,<div><br></div><div>I have some SAM/BAM files containing the alignments of some RNA-seq reads to hg19.  I&#39;m interested in calculating some mapping statistics, specifically, the percentage of reads mapping to exons, introns, and extragenic regions.  </div>
<div>I gather that this can be done with bedtools, but I&#39;m finding myself a little bit stuck just figuring out what files I need to get this information.  I gather that I need a GTF (or possibly GFF) file, and I downloaded one from the UCSC browser using the settings in the attached image.</div>
<div><br></div><div>The first couple lines of the resulting file are pasted below.  I see that the file has exon start and end sites.  Is there a way to get what I need with this file, or do I need something else? </div><div>
<br></div><div>Any assistance would be much appreciated,</div><div><br></div><div>Thanks</div><div><br></div><div>Alex</div><div><br></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
cat gencode.gtf | head -3</div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">#bin    name    chrom   strand  txStart txEnd   cdsStart        cdsEnd  exonCount       exonStarts      exonEnds        score   name2   cdsStartStat    cdsEndStat      exonFrames</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">0       ENST00000237247.6       chr1    +       66999065        67210057        67000041        67208778        27      66999065,66999928,67091529,67098752,67099762,67105459,67108492,67109226,67126195,67133212,67136677,67137626,67138963,67142686,67145360,67147551,67149789,67154830,67155872,67161116,67184976,67194946,67199430,67205017,67206340,67206954,67208755,      66999090,67000051,67091593,67098777,67099846,67105516,67108547,67109402,67126207,67133224,67136702,67137678,67139049,67142779,67145435,67148052,67149870,67154958,67155999,67161176,67185088,67195102,67199563,67205220,67206405,67207119,67210057,      0       SGIP1   cmpl    cmpl    -1,0,1,2,0,0,0,1,0,0,0,1,2,1,1,1,1,1,0,1,1,2,2,0,2,1,1,</div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">0       ENST00000371039.1       chr1    +       66999274        67210768        67000041        67208778        22      66999274,66999928,67091529,67098752,67105459,67108492,67109226,67136677,67137626,67138963,67142686,67145360,67154830,67155872,67160121,67184976,67194946,67199430,67205017,67206340,67206954,67208755,   66999355,67000051,67091593,67098777,67105516,67108547,67109402,67136702,67137678,67139049,67142779,67145435,67154958,67155999,67160187,67185088,67195102,67199563,67205220,67206405,67207119,67210768,   0       SGIP1   cmpl    cmpl    -1,0,1,2,0,0,1,0,1,2,1,1,1,0,1,1,2,2,0,2,1,1,</div>
</div>