Purpose: created BED files to visualize different transcripts on USSC browser from cufflinks output
How to Run: perl BEDfromTrancripts.pl -T transcripts_file.txt -L gencode.attributes.file.txt
The transcripts file is a typical output from cuffcompare:
8_00458540 XLOC_011348 FBXO2|FBXO2 x - - q3:AD2.974|AD2.974.1|100|6.152141|4.722721|7.581561|58.607883|430 q4:AD3.95|AD3.95.1|100|9.046277|5.273719|12.818835|21.328327|395 q5:AD4.565|AD4.565.1|100|9.136013|7.403165|10.868861|78.222360|461 q6:AD5.1346|AD5.1346.1|100|11.989985|10.757990|13.221980|128.213270|672 q7:AD6.286|AD6.286.1|100|9.181492|6.215037|12.147948|24.486141|438 q8:AD7.429|AD7.429.1|100|10.805550|9.351270|12.259830|77.007361|696 q9:AD8.809|AD8.809.1|100|13.744011|11.935960|15.552061|103.957922|568 q10:AD9.446|AD9.446.1|100|10.275882|8.469653|12.082110|51.629598|676 q11:AD10.329|AD10.329.1|100|2.582497|1.617748|3.547246|18.637065|360 q12:CT1.436|CT1.436.1|100|11.942306|10.506601|13.378011|125.901033|609 q13:CT2.840|CT2.840.1|100|10.398910|8.814966|11.982853|166.329675|456 q14:CT3.479|CT3.479.1|100|4.004266|3.202365|4.806167|59.372393|435 q15:CT4.346|CT4.346.1|100|6.608667|5.253728|7.963606|69.597980|365 q16:CT5.573|CT5.573.1|100|12.035976|10.546960|13.524992|110.168747|680 - q18:CT7.491|CT7.491.1|100|16.836556|13.956757|19.716356|110.514101|358 q19:CT8.464|CT8.464.1|100|36.136830|29.070582|43.203078|172.204315|299 q20:CT9.459|CT9.459.1|100|11.326804|8.865338|13.788270|84.022312|438 - q22:D1.447|D1.447.1|100|7.932166|6.075806|9.788525|60.498912|423 q23:D2.1805|D2.1805.1|100|2.149630|1.586002|2.713258|28.950735|449 q24:D3.1087|D3.1087.1|100|44.130410|38.356418|49.904403|277.076375|307 - q26:D5.610|D5.610.1|100|7.096536|5.524014|8.669059|49.536377|417 - q28:D7.730|D7.730.1|100|7.926554|6.696342|9.156766|59.980629|630 q29:D8.315|D8.315.2|55|1.928300|1.209276|2.647323|13.749436|629 q30:D9.482|D9.482.1|100|3.177128|2.382846|3.971410|20.911024|572 q31:D10.233|D10.233.1|100|7.543618|5.430982|9.656254|18.714736|572
The output is in a BED file which denotes exon-intron junctions. In addition, the transcript is color coded based on which group it is expressed in.
#lime if present in CT only
#blue if present in AD + CT only
#yellow if present in DLB only
#purple if present in AD + DLB
#teal if present in DLB + CT
#black if present in all three groups
chr1 11637558 11644939 8_00433015_AD1_CT2 500 + 11637558 11644939 0,0,255 5 38,294,97,135,1165 0,892,3353,3822,6216
1. go to this website <http://genome.ucsc.edu/cgi-bin/hgCustom?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg18&position=chr19%3A996%2C074-996%2C679&hgt.positionInput=enter+position%2C+gene+symbol+or+search+terms&hgt.suggestTrack=knownGene&hgsid=363174797>
2. place output
3. click submit
4. click on hyperlink under "pos"
5. zoom out to view full transcript