These are chat archives for cboursnell/transfuse

31st
Jan 2017
Roger Huerlimann
@RogerHuerlimann_twitter
Jan 31 2017 05:12

It looks like it's a transrate problem. Not sure which version of transrate is bundled with transfuse, but after reading some of the comments of Matt MacManes in the transrate thread it looks like the bad mapping is limited to transrate 1.0.3.
I ran transrate 1.0.1 on the second dataset show above and I get much better results than with 1.0.3, and more comparable to the transrate output of _cons.faproduced by transfuse. Strangely, this only seems to be an issue when I run transrate on the output of transfuse, but not when I run it on the trinity output.

[ INFO] 2017-01-31 14:31:31 : -----------------------------------
[ INFO] 2017-01-31 14:31:31 : fragments                   9955695
[ INFO] 2017-01-31 14:31:31 : fragments mapped            9119736
[ INFO] 2017-01-31 14:31:31 : p fragments mapped             0.92
[ INFO] 2017-01-31 14:31:31 : good mappings               7883571
[ INFO] 2017-01-31 14:31:31 : p good mapping                 0.79
[ INFO] 2017-01-31 14:31:31 : bad mappings                1236165
[ INFO] 2017-01-31 14:31:31 : potential bridges             14300
[ INFO] 2017-01-31 14:31:31 : bases uncovered             3231278
[ INFO] 2017-01-31 14:31:31 : p bases uncovered              0.03
[ INFO] 2017-01-31 14:31:31 : contigs uncovbase             49880
[ INFO] 2017-01-31 14:31:31 : p contigs uncovbase            0.36
[ INFO] 2017-01-31 14:31:31 : contigs uncovered               287
[ INFO] 2017-01-31 14:31:31 : p contigs uncovered             0.0
[ INFO] 2017-01-31 14:31:31 : contigs lowcovered           108491
[ INFO] 2017-01-31 14:31:31 : p contigs lowcovered           0.79
[ INFO] 2017-01-31 14:31:31 : contigs segmented              8238
[ INFO] 2017-01-31 14:31:31 : p contigs segmented            0.06
[ INFO] 2017-01-31 14:31:31 : Read metrics done in 4335 seconds
[ INFO] 2017-01-31 14:31:31 : No reference provided, skipping comparative diagnostics
[ INFO] 2017-01-31 14:31:31 : TRANSRATE ASSEMBLY SCORE     0.4622
[ INFO] 2017-01-31 14:31:31 : -----------------------------------
[ INFO] 2017-01-31 14:31:31 : TRANSRATE OPTIMAL SCORE      0.5372
[ INFO] 2017-01-31 14:31:31 : TRANSRATE OPTIMAL CUTOFF     0.5038
[ INFO] 2017-01-31 14:31:31 : good contigs                 102954
[ INFO] 2017-01-31 14:31:31 : p good contigs                 0.75

For completeness, this is the output when I run the _cons.fa file through transrate 1.0.3

[ INFO] 2017-01-31 14:33:07 : -----------------------------------
[ INFO] 2017-01-31 14:33:07 : fragments                   9955695
[ INFO] 2017-01-31 14:33:07 : fragments mapped            4729856
[ INFO] 2017-01-31 14:33:07 : p fragments mapped             0.48
[ INFO] 2017-01-31 14:33:07 : good mappings               4034657
[ INFO] 2017-01-31 14:33:07 : p good mapping                 0.41
[ INFO] 2017-01-31 14:33:07 : bad mappings                 695199
[ INFO] 2017-01-31 14:33:07 : potential bridges                 0
[ INFO] 2017-01-31 14:33:07 : bases uncovered            60814931
[ INFO] 2017-01-31 14:33:07 : p bases uncovered              0.48
[ INFO] 2017-01-31 14:33:07 : contigs uncovbase             69981
[ INFO] 2017-01-31 14:33:07 : p contigs uncovbase             0.5
[ INFO] 2017-01-31 14:33:07 : contigs uncovered            140035
[ INFO] 2017-01-31 14:33:07 : p contigs uncovered             1.0
[ INFO] 2017-01-31 14:33:07 : contigs lowcovered           140035
[ INFO] 2017-01-31 14:33:07 : p contigs lowcovered            1.0
[ INFO] 2017-01-31 14:33:07 : contigs segmented             13130
[ INFO] 2017-01-31 14:33:07 : p contigs segmented            0.09
[ INFO] 2017-01-31 14:33:07 : Read metrics done in 4308 seconds
[ INFO] 2017-01-31 14:33:07 : No reference provided, skipping comparative diagnostics
[ INFO] 2017-01-31 14:33:41 : TRANSRATE ASSEMBLY SCORE      0.132
[ INFO] 2017-01-31 14:33:41 : -----------------------------------
[ INFO] 2017-01-31 14:33:41 : TRANSRATE OPTIMAL SCORE      0.2154
[ INFO] 2017-01-31 14:33:41 : TRANSRATE OPTIMAL CUTOFF     0.3812
[ INFO] 2017-01-31 14:33:42 : good contigs                  89018
[ INFO] 2017-01-31 14:33:42 : p good contigs                 0.64