Format of files in this directory (running head).
OID40453_annotation.gff
C16582 TJGR_v9 transcripts 35 385 -1 . . ID=CGI_10000001; color=000000
C17212 TJGR_v9 transcripts 31 363 +1 . . ID=CGI_10000002; color=000000
C17316 TJGR_v9 transcripts 30 257 +1 . . ID=CGI_10000003; color=000000
C17476 TJGR_v9 transcripts 34 257 -1 . . ID=CGI_10000004; color=000000
C17998 TJGR_v9 transcripts 196 387 -1 . . ID=CGI_10000005; color=000000
C18346 TJGR_v9 transcripts 174 551 +1 . . ID=CGI_10000009; color=000000
C18428 TJGR_v9 transcripts 286 546 -1 . . ID=CGI_10000010; color=000000
C18964 TJGR_v9 transcripts 203 658 -1 . . ID=CGI_10000011; color=000000
C18980 TJGR_v9 transcripts 30 674 +1 . . ID=CGI_10000012; color=000000
C19100 TJGR_v9 transcripts 160 681 -1 . . ID=CGI_10000013; color=000000
OID40453_probe_locations.gff
scaffold1 NGS OID40453_probe_locations 52347 52396 1 color=000000
scaffold1 NGS OID40453_probe_locations 52472 52521 1 color=000000
scaffold1 NGS OID40453_probe_locations 52597 52649 1 color=000000
scaffold1 NGS OID40453_probe_locations 52741 52797 1 color=000000
scaffold1 NGS OID40453_probe_locations 52851 52915 1 color=000000
scaffold1 NGS OID40453_probe_locations 52996 53056 1 color=000000
scaffold1 NGS OID40453_probe_locations 53101 53152 1 color=000000
scaffold1 NGS OID40453_probe_locations 53241 53290 2 color=000000
scaffold1 NGS OID40453_probe_locations 53351 53405 1 color=000000
scaffold1 NGS OID40453_probe_locations 53476 53534 1 color=000000
OID40453_probes.txt (zip version)
PROBE_SEQUENCE PROBE_ID SEQ_ID POSITION DESIGN_NOTE SELECTION_CRITERIA PROBE_CLASS PROBE_TM FREQUENCY COUNT RULES SLOPE RSQUARED GENOMIC COT1 SNP_COUNT SCORE RANK
CGATTAGTGGACGTGAGAATTCTCAAGAGCACACCGTGTGTATACATCAC scaffold39960:+:29315 scaffold39960:29300-48043 29315 target_tm:76.00;probe_tm:76.80;freq: 3.28;count:01;rules:0000;score:0991 experimental 76.80 3.28 0 0.00 0.00 0.00 0.00 0 991 1
TTTGTTGGAGCTGTATAATAAATGAAACTGAAACCAATGAATTCTTATTGAATTCAAC scaffold39960:+:29445 scaffold39960:29300-48043 29445 target_tm:76.00;probe_tm:70.90;freq:13.30;count:01;rules:0000;score:0804 experimental 70.90 13.30 1 0 0.00 0.00 0.00 0.00 0 804 1
CCTTTGCCTTTTTTTCAAAAATGCAATGCTTGTCAAGATGTTTTAGATGAAGCTGTGG scaffold39960:+:29572 scaffold39960:29300-48043 29572 target_tm:76.00;probe_tm:74.40;freq:19.66;count:01;rules:-350;score:0496 experimental 74.40 19.66 1 -350 0.00 0.00 0.00 0.00 0 496 1
CATTTCCTATTTCCTCATCTTAATAATAGCCAAGGGTTTTTAGTCCACTTTGCTC scaffold39960:+:29677 scaffold39960:29300-48043 29677 target_tm:76.00;probe_tm:73.90;freq: 6.46;count:01;rules:0000;score:0916 experimental 73.90 6.46 0 0.00 0.00 0.00 0.00 0 916 1
AAATGCCTTTGATTTTGGATCTTTATATAACAAATACAATTCATAATTTGACTGTT scaffold39960:+:29807 scaffold39960:29300-48043 29807 target_tm:76.00;probe_tm:68.70;freq:24.29;count:04;rules:0000;score:0417 experimental 68.70 24.29 4 0 0.00 0.00 0.00 0.00 0 417 1
TTTTAGTCATATATTTATACAACTAAGGTGAAAGAAAAGACTAAAGTTTCCT scaffold39960:+:29947 scaffold39960:29300-48043 29947 target_tm:76.00;probe_tm:68.60;freq: 8.53;count:01;rules:0000;score:0790 experimental 68.60 8.53 0 0.00 0.00 0.00 0.00 0 790 1
OID40453_stats.txt
SEQ_ID LENGTH PROBES DENSITY MEAN_INTERVAL MEDIAN_INTERVAL 1ST_QUARTILE 3RD_QUARTILE MIN_INTERVAL MAX_INTERVAL COVERAGE
scaffold1:52347-57631 5285 43 122 125 125 120 132 105 150 2384
scaffold1:161989-185527 23539 171 137 125 125 120 140 105 451 9819
scaffold1:207337-231800 24464 176 139 125 125 115 137 105 813 9926
scaffold3:65419-71497 6079 47 129 126 127 115 136 105 200 2660
scaffold3:72058-78354 6297 43 146 126 130 115 140 105 602 2511
scaffold3:82418-120562 38145 248 153 124 125 115 140 105 1071 14107
scaffold3:122297-131079 8783 66 133 125 125 120 135 102 557 3814
121101_OysterV9_MG_meth.pos
PROBE_ID SEQ_ID CHROMOSOME POSITION COUNT LENGTH GC
scaffold1:+:52347 scaffold1:52347-57631 scaffold1 52347 1 50 0.44
scaffold1:+:52472 scaffold1:52347-57631 scaffold1 52472 1 50 0.44
scaffold1:+:52597 scaffold1:52347-57631 scaffold1 52597 1 53 0.28
scaffold1:+:52741 scaffold1:52347-57631 scaffold1 52741 1 57 0.30
scaffold1:+:52851 scaffold1:52347-57631 scaffold1 52851 1 65 0.34
scaffold1:+:52996 scaffold1:52347-57631 scaffold1 52996 1 61 0.38
scaffold1:+:53101 scaffold1:52347-57631 scaffold1 53101 1 52 0.42
scaffold1:+:53241 scaffold1:52347-57631 scaffold1 53241 2 50 0.46
scaffold1:+:53351 scaffold1:52347-57631 scaffold1 53351 1 55 0.40
121101_OysterV9_MG_meth.ProbeAnnotation.rda
R object - no preview- annotation object.
oyster.v9.glean.final.rename.mRNA.gff
C16582 GLEAN mRNA 35 385 0.555898 - . ID=CGI_10000001;
C17212 GLEAN mRNA 31 363 0.999572 + . ID=CGI_10000002;
C17316 GLEAN mRNA 30 257 0.555898 + . ID=CGI_10000003;
C17476 GLEAN mRNA 34 257 0.998947 - . ID=CGI_10000004;
C17998 GLEAN mRNA 196 387 1 - . ID=CGI_10000005;
C18346 GLEAN mRNA 174 551 1 + . ID=CGI_10000009;
C18428 GLEAN mRNA 286 546 0.555898 - . ID=CGI_10000010;
C18964 GLEAN mRNA 203 658 0.999572 - . ID=CGI_10000011;
C18980 GLEAN mRNA 30 674 0.555898 + . ID=CGI_10000012;
C19100 GLEAN mRNA 160 681 0.999955 - . ID=CGI_10000013;
2013.09.24.targets.txt
FileNameCy5 FileNameCy3
A01_EE2.input_532.pair A01_Ctrl.input_635.pair
A02_EE2.MBD_532.pair A02_Ctrl.MBD_635.pair
A03_EE2.MBD_635.pair A03_Ctrl.MBD_532.pair
spottypes.txt
SpotType GENE_EXPR_OPTION PROBE_ID Color
BLOCK1 BLOCK1 * black
RANDOM RANDOM * grey