Mercurial > repos > jjohnson > cummerbund

view test-data/cuffdiff_out1.txt @ 3:f109453ecfa2

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
author Jim Johnson <jj@umn.edu>
date Fri, 15 Nov 2013 13:39:14 -0600
parents fdf01b3c1841
children
line wrap: on
line source

test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
TCONS_00000001	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
TCONS_00000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
TCONS_00000003	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000009	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	5.68095e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
TCONS_00000010	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.15515e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
TCONS_00000011	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000012	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.02976e+06	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
TCONS_00000013	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
TCONS_00000014	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000015	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000016	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000017	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000018	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000019	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000020	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	959058	705514	-0.442943	0.376027	0.706897	1	no
TCONS_00000021	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000022	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	77513.9	285108	1.87898	-1.76152	0.0781506	1	no
TCONS_00000023	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000024	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
TCONS_00000025	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.4671e+07	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
TCONS_00000026	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	3.99739e+06	1.82908e+06	-1.12794	0.781831	0.434314	1	no
TCONS_00000027	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	56312.4	372827	2.72698	-1.67622	0.0936947	1	no
TCONS_00000028	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	2.66226e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
TCONS_00000029	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.0951e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
TCONS_00000030	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.06814e+09	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
TCONS_00000031	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000033	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.29576e+07	1.79769e+308	1.79769e+308	0.158655	0.158655	no
TCONS_00000034	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	9.79535e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
TCONS_00000037	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000038	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000039	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000040	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000041	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000042	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000043	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000044	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000045	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000046	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000047	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000048	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000049	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000050	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000051	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000052	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000053	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000054	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	368900	429265	0.21864	-0.483034	0.629072	1	no
TCONS_00000055	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	404373	338500	-0.25653	0.342922	0.731657	1	no
TCONS_00000056	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	402276	686974	0.772069	-1.24554	0.212932	1	no
TCONS_00000057	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	3.994e+06	2.93812e+06	-0.442943	0.217099	0.828131	1	no
TCONS_00000058	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000059	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000060	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000062	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000063	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000065	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.89853e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
TCONS_00000066	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.31744e+07	0	-1.79769e+308	-1.79769e+308	0.0416323	0.150149	no
TCONS_00000067	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000068	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	4.39147e+06	0	-1.79769e+308	-1.79769e+308	0.158655	1	no
TCONS_00000069	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	1.36901e+06	0	0	0	1	1	no
TCONS_00000070	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000071	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000072	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000073	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	9.99919e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
TCONS_00000074	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000075	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000076	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	265614	41870.3	-2.66534	2.48499	0.0129556	1	no
TCONS_00000077	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000078	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000079	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000080	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000081	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000082	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000083	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.8095e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
TCONS_00000084	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	342218	75524	-2.17991	1.96162	0.049807	1	no
TCONS_00000085	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	937403	137917	-2.76487	1.66807	0.0953024	1	no
TCONS_00000086	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000087	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000088	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000089	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000090	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	8.91489e+06	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
TCONS_00000091	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	585828	0	-1.79769e+308	-1.79769e+308	0.0512352	1	no
TCONS_00000092	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.19208e+08	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
TCONS_00000093	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	4.42166e+06	0	-1.79769e+308	-1.79769e+308	0.0786496	1	no
TCONS_00000094	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	4.28358e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
TCONS_00000095	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	7.29939e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
TCONS_00000096	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000097	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000098	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000099	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
TCONS_00000100	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no