geneid docs

1. geneid (default) format

## date Thu Sep 27 15:21:50 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Acceptors(+) predicted in sequence test: [0,99999]
Acceptor        1        2       0.40   +       ***********************GATC
Acceptor        6        7      -0.01   +       ******************GATCAGGCT
Acceptor       60       61       2.21   +       GCATTCTTTTCTGCTTCAATTCAGTCC
Acceptor       83       84      -0.79   +       GTCCATCCCTGACCACCCACCCAGCCA
Acceptor      140      141       4.62   +       TCCTCCACCTTCCCACTCCCACAGCTA
Acceptor      151      152      -6.25   +       CCCACTCCCACAGCTAATCAGTAGCCA
Acceptor      164      165      -1.79   +       CTAATCAGTAGCCAAACCCTTTAGATT
Acceptor      229      230       0.87   +       TCCTCTAATTATGACTTAATTCAGGCT
Acceptor      272      273       2.02   +       TAAATTATTGCTGTATTGCTACAGGAG
Acceptor      275      276      -6.95   +       ATTATTGCTGTATTGCTACAGGAGTGG
Acceptor      316      317       1.17   +       ACTGTTCATCTTGGTATGCTATAGACT
Acceptor      328      329      -4.24   +       GGTATGCTATAGACTCTTGCCCAGCAG
Acceptor      331      332      -1.50   +       ATGCTATAGACTCTTGCCCAGCAGTTT
Acceptor      353      354       0.15   +       AGTTTTGCCTCAATTCTTTAAAAGCTC
Acceptor      359      360      -4.31   +       GCCTCAATTCTTTAAAAGCTCCAGTTC
Acceptor      383      384      -0.88   +       TTCATTGTTTGAAATATCAATCAGAAC
Acceptor      424      425       0.88   +       GCTAAAATGATTGTCATTCCCCAGTTT
Acceptor      450      451      -0.95   +       TTAATATCTCTATCATCTGCTAAGTAA
Acceptor      456      457      -5.79   +       TCTCTATCATCTGCTAAGTAAAAGCAA
Acceptor      478      479      -0.15   +       AGCAAGCTCCTCCTTGTGGCGTAGCAG
Acceptor      481      482      -0.48   +       AAGCTCCTCCTTGTGGCGTAGCAGGGC
...

% bin/geneid -P param/human3iso.param -ao test.fa

2. gff format

## gff-version 2 ## date Thu Sep 27 15:24:22 2003 ## source-version: geneid v 1.2 -- geneid@imim.es ## Sequence test - Length = 198285 bps # Acceptors(+) predicted in sequence test: [0,99999] test geneid_v1.2 Acceptor 1 2 0.40 + . # ***********************GATC test geneid_v1.2 Acceptor 6 7 -0.01 + . # ******************GATCAGGCT test geneid_v1.2 Acceptor 60 61 2.21 + . # GCATTCTTTTCTGCTTCAATTCAGTCC test geneid_v1.2 Acceptor 83 84 -0.79 + . # GTCCATCCCTGACCACCCACCCAGCCA test geneid_v1.2 Acceptor 140 141 4.62 + . # TCCTCCACCTTCCCACTCCCACAGCTA test geneid_v1.2 Acceptor 151 152 -6.25 + . # CCCACTCCCACAGCTAATCAGTAGCCA test geneid_v1.2 Acceptor 164 165 -1.79 + . # CTAATCAGTAGCCAAACCCTTTAGATT test geneid_v1.2 Acceptor 229 230 0.87 + . # TCCTCTAATTATGACTTAATTCAGGCT test geneid_v1.2 Acceptor 272 273 2.02 + . # TAAATTATTGCTGTATTGCTACAGGAG test geneid_v1.2 Acceptor 275 276 -6.95 + . # ATTATTGCTGTATTGCTACAGGAGTGG test geneid_v1.2 Acceptor 316 317 1.17 + . # ACTGTTCATCTTGGTATGCTATAGACT test geneid_v1.2 Acceptor 328 329 -4.24 + . # GGTATGCTATAGACTCTTGCCCAGCAG test geneid_v1.2 Acceptor 331 332 -1.50 + . # ATGCTATAGACTCTTGCCCAGCAGTTT test geneid_v1.2 Acceptor 353 354 0.15 + . # AGTTTTGCCTCAATTCTTTAAAAGCTC test geneid_v1.2 Acceptor 359 360 -4.31 + . # GCCTCAATTCTTTAAAAGCTCCAGTTC test geneid_v1.2 Acceptor 383 384 -0.88 + . # TTCATTGTTTGAAATATCAATCAGAAC test geneid_v1.2 Acceptor 424 425 0.88 + . # GCTAAAATGATTGTCATTCCCCAGTTT test geneid_v1.2 Acceptor 450 451 -0.95 + . # TTAATATCTCTATCATCTGCTAAGTAA test geneid_v1.2 Acceptor 456 457 -5.79 + . # TCTCTATCATCTGCTAAGTAAAAGCAA test geneid_v1.2 Acceptor 478 479 -0.15 + . # AGCAAGCTCCTCCTTGTGGCGTAGCAG ...

% bin/geneid -P param/human3iso.param -aoG test.fa