Table 1 Software used in the comparison

2.07

CA/IA, no annotation

http://tophat.cbcb.umd.edu/

[28, 29]

1.2.3

1

http://deweylab.biostat.wisc.edu/rsem/

[19, 35]

2.0.2

1,2,3

http://cufflinks.cbcb.umd.edu/

[20]

May 7th, 2012

1,2

https://sites.google.com/site/jingyijli/

[21]

0.9.1

1,2,3

http://alumni.cs.ucr.edu/~liw/cem.html

[23]

1.0.7

2

http://compbio.cs.toronto.edu/ireckon/

[22]