Mercurial > repos > jjohnson > cummerbund
view test-data/cuffdiff_out6.txt @ 3:f109453ecfa2
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 |
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tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status XLOC_000001 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK XLOC_000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK XLOC_000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK XLOC_000004 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK XLOC_000005 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK XLOC_000006 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK XLOC_000007 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 368900 151353 586447 OK 429265 337221 521309 OK XLOC_000008 - - XLOC_000008 - TSS11 chr1:3190858-3191434 - - 404373 101434 707312 OK 338500 95761.5 581239 OK XLOC_000009 - - XLOC_000009 - TSS12 chr1:3191512-3192077 - - 402276 96829.4 707722 OK 686974 410563 963384 OK XLOC_000010 - - XLOC_000010 - TSS15 chr1:3192250-3192336 - - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK XLOC_000011 - - XLOC_000011 - TSS16 chr1:3192441-3192494 - - 0 0 0 OK 5.68095e+07 0 1.3715e+08 OK XLOC_000012 - - XLOC_000012 - TSS17 chr1:3192550-3192629 - - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK XLOC_000013 - - XLOC_000013 - TSS18 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK XLOC_000014 - - XLOC_000014 - TSS19 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK XLOC_000015 - - XLOC_000015 - TSS20 chr1:3192940-3193042 - - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK XLOC_000016 - - XLOC_000016 - TSS21 chr1:3194185-3194226 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK XLOC_000017 - - XLOC_000017 - TSS22 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK XLOC_000018 - - XLOC_000018 - TSS23 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK XLOC_000019 - - XLOC_000019 - TSS24 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK XLOC_000020 - - XLOC_000020 - TSS25 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK XLOC_000021 - - XLOC_000021 - TSS26 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK XLOC_000022 - - XLOC_000022 - TSS27 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK XLOC_000023 - - XLOC_000023 - TSS28 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK XLOC_000024 - - XLOC_000024 - TSS29 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK XLOC_000025 - - XLOC_000025 - TSS30 chr1:3200022-3200191 - - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK XLOC_000026 - - XLOC_000026 - TSS32 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK XLOC_000027 - - XLOC_000027 - TSS33 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK XLOC_000028 - - XLOC_000028 - TSS34 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK XLOC_000029 - - XLOC_000029 - TSS35 chr1:3201077-3201481 - - 77513.9 0 167019 OK 285108 21736.5 548480 OK XLOC_000030 - - XLOC_000030 - TSS37 chr1:3201596-3201666 - - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK XLOC_000031 - - XLOC_000031 - TSS38 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK XLOC_000032 - - XLOC_000032 - TSS39 chr1:3201725-3201809 - - 1.31744e+07 0 2.83869e+07 OK 0 0 0 OK XLOC_000033 - - XLOC_000033 Xkr4 TSS40 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK XLOC_000034 - - XLOC_000034 Xkr4 TSS41 chr1:3212213-3212292 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK XLOC_000035 - - XLOC_000035 Xkr4 TSS42 chr1:3212367-3212439 - - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK XLOC_000036 - - XLOC_000036 Xkr4 TSS43 chr1:3212717-3212801 - - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK XLOC_000037 - - XLOC_000037 Xkr4 TSS44,TSS45 chr1:3213095-3213242 - - 5.3664e+06 0 1.39795e+07 LOWDATA 1.82908e+06 0 5.48723e+06 OK XLOC_000038 - - XLOC_000038 Xkr4 TSS46 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK XLOC_000039 - - XLOC_000039 Xkr4 TSS47 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK XLOC_000040 - - XLOC_000040 Xkr4 TSS48 chr1:3242633-3242923 - - 56312.4 0 168937 OK 372827 0 761430 OK XLOC_000041 - - XLOC_000041 Xkr4 TSS49 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK XLOC_000042 - - XLOC_000042 Xkr4 TSS50 chr1:3243018-3243079 - - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK XLOC_000043 - - XLOC_000043 Xkr4 TSS51 chr1:3243108-3243154 - - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK XLOC_000044 - - XLOC_000044 Xkr4 TSS52 chr1:3243347-3243401 - - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK XLOC_000045 - - XLOC_000045 Xkr4 TSS53 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK XLOC_000046 - - XLOC_000046 Xkr4 TSS54 chr1:3256974-3257011 - - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK XLOC_000047 - - XLOC_000047 Xkr4 TSS55 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK XLOC_000048 - - XLOC_000048 Xkr4 TSS56 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK XLOC_000049 - - XLOC_000049 Xkr4 TSS57 chr1:3277913-3278390 - - 265614 16793 514436 OK 41870.3 0 90217.9 OK XLOC_000050 - - XLOC_000050 Xkr4 TSS59 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK XLOC_000051 - - XLOC_000051 Xkr4 TSS60 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK XLOC_000052 - - XLOC_000052 Xkr4 TSS61 chr1:3280686-3280741 - - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK XLOC_000053 - - XLOC_000053 Xkr4 TSS62 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK XLOC_000054 - - XLOC_000054 Xkr4 TSS63 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK XLOC_000055 - - XLOC_000055 Xkr4 TSS64 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK XLOC_000056 - - XLOC_000056 Xkr4 TSS65 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK XLOC_000057 - - XLOC_000057 Xkr4 TSS66 chr1:3290488-3290553 - - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK XLOC_000058 - - XLOC_000058 Xkr4 TSS67 chr1:3290798-3290859 - - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK XLOC_000059 - - XLOC_000059 Xkr4 TSS68 chr1:3290919-3291273 - - 342218 0 691214 OK 75524 0 162732 OK XLOC_000060 - - XLOC_000060 Xkr4 TSS70,TSS71 chr1:3299443-3299664 - - 937403 0 1.99795e+06 OK 137917 0 413751 OK XLOC_000061 - - XLOC_000061 Xkr4 TSS72 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK XLOC_000062 - - XLOC_000062 Xkr4 TSS73 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK XLOC_000063 - - XLOC_000063 Xkr4 TSS74 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK XLOC_000064 - - XLOC_000064 Xkr4 TSS75 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK XLOC_000065 - - XLOC_000065 Xkr4 TSS76 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK XLOC_000066 - - XLOC_000066 Xkr4 TSS77 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK XLOC_000067 - - XLOC_000067 Xkr4 TSS78 chr1:3351240-3351311 - - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK XLOC_000068 - - XLOC_000068 Xkr4 TSS79,TSS80 chr1:3355887-3356119 - - 585828 0 1.30332e+06 OK 0 0 0 OK XLOC_000069 - - XLOC_000069 Xkr4 TSS81 chr1:3356180-3356225 - - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK XLOC_000070 - - XLOC_000070 Xkr4 TSS82 chr1:3363076-3363176 - - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK XLOC_000071 - - XLOC_000071 Xkr4 TSS83 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK XLOC_000072 - - XLOC_000072 Xkr4 TSS84 chr1:3363387-3363446 - - 4.28358e+07 0 1.03415e+08 OK 0 0 0 OK XLOC_000073 - - XLOC_000073 Xkr4 TSS85 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK XLOC_000074 - - XLOC_000074 Xkr4 TSS86 chr1:3364871-3364919 - - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK XLOC_000075 - - XLOC_000075 Xkr4 TSS87 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK XLOC_000076 - - XLOC_000076 Xkr4 TSS88 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK XLOC_000077 - - XLOC_000077 Xkr4 TSS89 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK XLOC_000078 - - XLOC_000078 Xkr4 TSS90 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK XLOC_000079 - - XLOC_000079 Xkr4 TSS91 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK XLOC_000080 - - XLOC_000080 Xkr4 TSS92 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK XLOC_000081 - - XLOC_000081 Xkr4 TSS93 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK XLOC_000082 - - XLOC_000082 Xkr4 TSS94 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK XLOC_000083 - - XLOC_000083 Xkr4 TSS95 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK XLOC_000084 - - XLOC_000084 Xkr4 TSS96 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK XLOC_000085 - - XLOC_000085 Xkr4 TSS97 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK XLOC_000086 - - XLOC_000086 Xkr4 TSS98 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK XLOC_000087 - - XLOC_000087 Xkr4 TSS99 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK