These are chat archives for cboursnell/transfuse

27th
Jan 2017
Roger Huerlimann
@RogerHuerlimann_twitter
Jan 27 2017 06:11

@cboursnell Sorry for posting yet another query. I compared the transrate scores of the _cons.fa file that transfuse automatically creates with a manual transrate analysis I ran on the final output file. I expected them to be fairly similar since both analyses use the same reads for the mapping and both files should be very similar. However, the transrate results for _cons.fa are much better than what I get for the final output file. Any ideas what the problem could be?

>cat Transfuse_output_cons_stats.txt
fragments         9955695
fragments_mapped        9116349
p_fragments_mapped      0.9156918728426293
good_mappings   7881454
p_good_mapping  0.7916528178093041
bad_mappings    1234895
potential_bridges       14537
bases_uncovered 4923627
p_bases_uncovered       0.03910550080631024
contigs_uncovbase       51971
p_contigs_uncovbase     0.3711286464098261
contigs_uncovered       1846
p_contigs_uncovered     0.013182418681044025
contigs_lowcovered      110466
p_contigs_lowcovered    0.7888456457314242
contigs_segmented       8378
p_contigs_segmented     0.05982790016781519
assembly score: 0.44934868372400943
optimal score : 0.5368280402996235
cutoff        : 0.4987261911265521

And this is result of manual transrate analysis of the final output file from transfuse:

[ INFO] 2017-01-27 12:34:47 : -----------------------------------
[ INFO] 2017-01-27 12:34:47 : fragments                   9955695
[ INFO] 2017-01-27 12:34:47 : fragments mapped            4834496
[ INFO] 2017-01-27 12:34:47 : p fragments mapped             0.49
[ INFO] 2017-01-27 12:34:47 : good mappings               4124619
[ INFO] 2017-01-27 12:34:47 : p good mapping                 0.41
[ INFO] 2017-01-27 12:34:47 : bad mappings                 709877
[ INFO] 2017-01-27 12:34:47 : potential bridges                 0
[ INFO] 2017-01-27 12:34:47 : bases uncovered            57553164
[ INFO] 2017-01-27 12:34:47 : p bases uncovered              0.47
[ INFO] 2017-01-27 12:34:47 : contigs uncovbase             67609
[ INFO] 2017-01-27 12:34:47 : p contigs uncovbase            0.49
[ INFO] 2017-01-27 12:34:47 : contigs uncovered            138052
[ INFO] 2017-01-27 12:34:47 : p contigs uncovered             1.0
[ INFO] 2017-01-27 12:34:47 : contigs lowcovered           138052
[ INFO] 2017-01-27 12:34:47 : p contigs lowcovered            1.0
[ INFO] 2017-01-27 12:34:47 : contigs segmented             13159
[ INFO] 2017-01-27 12:34:47 : p contigs segmented             0.1
[ INFO] 2017-01-27 12:34:47 : Read metrics done in 1545 seconds
[ INFO] 2017-01-27 12:34:47 : No reference provided, skipping comparative diagnostics
[ INFO] 2017-01-27 12:35:31 : TRANSRATE ASSEMBLY SCORE     0.1434
[ INFO] 2017-01-27 12:35:31 : -----------------------------------
[ INFO] 2017-01-27 12:35:31 : TRANSRATE OPTIMAL SCORE      0.2202
[ INFO] 2017-01-27 12:35:31 : TRANSRATE OPTIMAL CUTOFF     0.3812
[ INFO] 2017-01-27 12:35:32 : good contigs                  89448
[ INFO] 2017-01-27 12:35:32 : p good contigs                 0.65