Table 4
Number of transcripts assembled (TA) with Cufflinks and the percentage they represent in each sample
Code L1 L2 L3 L4 L5 H1 H2 H3 H4 H5
TA % TA % TA % TA % TA % TA % TA % TA % TA % TA %
= 1971 8.7 2486 10.4 2526 11 2244 9.2 2762 10.2 2642 10.1 2363 9.4 2761 9.9 2119 10.4 2838 10.5
c 4059 17.8 4202 17.6 3953 17.2 4203 17.3 4289 15.9 3955 15.1 4083 16.3 4183 15.0 3569 17.5 3961 14.7
e 745 3.3 508 2.1 518 2.3 672 2.8 576 2.1 616 2.4 736 2.9 604 2.2 489 2.4 529 2.0
i 3115 13.7 2719 11.4 2629 11.4 3153 13.0 3248 12.0 3301 12.6 3373 13.5 3637 13.1 2250 11.0 3234 12.0
j 4348 19.1 4709 19.7 4436 19.3 4666 19.2 5373 19.9 5288 20.2 4833 19.3 5658 20.3 3488 17.1 5428 20.1
o 1067 4.7 1175 4.9 1139 5.0 1157 4.8 1237 4.6 1142 4.4 1154 4.6 1170 4.2 1129 5.5 1204 4.5
p 1570 6.9 1656 6.9 1566 6.8 1682 6.9 1635 6.1 1603 6.1 1606 6.4 1676 6.0 1699 8.3 1598 5.9
s 60 0.3 77 0.3 72 0.3 76 0.3 94 0.4 86 0.3 71 0.3 72 0.3 68 0.3 100 0.4
u 4447 19.5 4560 19.1 4541 19.7 4789 19.7 5468 20.2 5456 20.9 5089 20.3 5680 20.4 4421 21.7 5638 20.9
x 1392 6.1 1838 7.7 1630 7.1 1663 6.8 2346 8.7 2066 7.9 1761 7.0 2415 8.7 1192 5.8 2496 9.2
Total 22774 100 23930 100 23010 100 24305 100 27028 100 26155 100 25069 100 27856 100 20424 100 27026 100

Class codes described by Cuffcompare: "=" Exactly equal to the reference annotation, "c " Contained in the reference annotation, "e" possible pre-mRNA molecule, "i " An exon falling into an intron of the reference, "j " New isoforms, "o" Unknown, generic overlap with reference, "p" Possible polymerase run-on fragment, “s” An intron of the transfrag overlapping a reference intron on the opposite strand, "u" Unknown, intergenic transcript, “x” Exonic overlap with reference on the opposite strand. L1 to L5 and H1 to H5 correspond to animals of the L and H groups, respectively.

Ramayo-Caldas et al. BMC Genomics 2012 13:547   doi:10.1186/1471-2164-13-547

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