how does cufflinks work when you supply it with a gtf file. I used the knownGenes UCSC gtf for mm9. When I run Cufflinks w/o a gtf and then run Cuffcompare with a gtf I get the results below for chromosome M.
cufflinks w/o gtf file
then running cuffcompare w/ gtf file on the above file shows
When I run Cufflinks with a gtf I get this
cufflinks w/ gtf file
How does Cufflinks utilize the gtf file? The Cufflinks w/o the gtf then Cuffcompare w/ gtf shows 4 unique trans_id for chrM, the Cufflinks w/ gtf shows 8 unique trans_id; in addition, the Cufflinks w/ gtf shows coordinates that are not present in the transcripts.expr of the Cufflinks ran w/o gtf, where did they come from? Thanks.
Either one of the output is generating extra information or one of them is missing information, and I believe the latter to be true because the coverage.wig file from UCSC shows that the genes such as ATPase6 is present so how come it is not showing up in Cufflinks that is ran w/o the gtf file? Any insight would be helpful.
http://genome.ucsc.edu/cgi-bin/hgTra...varRep_close=0
cufflinks w/o gtf file
Code:
CUFF.213872.1 859088 chrM 121 953 873.319 1 1 862.495 884.143 1627.3 832 CUFF.213874.1 859088 chrM 1148 2623 746.907 1 1 739.389 754.425 1391.83 1475 CUFF.213876.1 859088 chrM 2726 3681 1593.64 1 1 1580 1607.29 2969.6 955 CUFF.213878.1 859088 chrM 3934 4923 884.824 1 1 874.831 894.817 1648.73 989 CUFF.213880.1 859088 chrM 15416 16059 260.697 1 1 253.97 267.424 485.81 643
Code:
uc009vev.1 uc009vev.1 = CUFF.213872 CUFF.213872.1 100 873.319096 862.495228 884.142963 1627.300787 832 CUFF.213872.1 uc009vew.1 uc009vew.1 c CUFF.213876 CUFF.213876.1 100 1593.642682 1579.995234 1607.290129 2969.596078 955 CUFF.213876.1 uc009vew.1 uc009vew.1 = CUFF.213874 CUFF.213874.1 100 746.907244 739.389371 754.425116 1391.830367 1475 CUFF.213874.1 uc009vex.1 uc009vex.1 = CUFF.213878 CUFF.213878.1 100 884.824253 874.831434 894.817071 1648.729185 989 CUFF.213878.1 uc009vfc.1 uc009vfc.1 p CUFF.213880 CUFF.213880.1 100 260.696876 253.969897 267.423855 485.810439 643 CUFF.213880.1
cufflinks w/ gtf file
Code:
uc009vev.1 602582 chrM 69 852 840.341 1 1 829.397 851.286 1565.84 783 uc009vew.1 602582 chrM 1148 3703 1018.15 1 1 1011.48 1024.82 1897.25 2555 uc009vex.1 602582 chrM 3848 4933 794.654 1 1 785.613 803.696 1480.72 1085 uc009vey.1 602582 chrM 5326 6938 4153.36 1 1 4136.4 4170.32 7739.4 1612 uc009vez.1 602582 chrM 7009 7699 1493.21 1 1 1477.67 1508.76 2782.55 690 uc009vfa.1 602582 chrM 7765 8607 1599.36 1 1 1584.8 1613.92 2980.3 842 uc009vfb.1 602582 chrM 9875 11542 1003.56 1 1 995.359 1011.75 1870.08 1667 uc009vfc.1 602582 chrM 12405 15288 1279.48 1 1 1272.44 1286.52 2384.19 2883
Either one of the output is generating extra information or one of them is missing information, and I believe the latter to be true because the coverage.wig file from UCSC shows that the genes such as ATPase6 is present so how come it is not showing up in Cufflinks that is ran w/o the gtf file? Any insight would be helpful.
http://genome.ucsc.edu/cgi-bin/hgTra...varRep_close=0
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