TRIP - T cell receptor/immunoglobulin profiler

BMC Bioinformatics

Table 1 Comparison of the results of the preselection and selection processes using the Galaxy and the TRIP tools

	T3396 GALAXY	%	T3396 TRIP	%	T3397 GALAXY	%	T3397 TRIP	%	T3404 GALAXY	%	T3404 TRIP	%
Total reads of raw data	348529	100	348529	100	372814	100	372814	100	296088	100	296088	100
Functional TRBV	340758	97.8	346629	99.5	367404	98.5	372014	99.8	289175	97.7	295277	99.7
filter out	1878	0.5	1900	0.5	796	0.2	800	0.2	772	0.3	811	0.3
Not Containing X,#,*	329344	94.5	335215	96.2	357235	95.8	361845	97.1	282510	95.4	288612	97.5
filter out	11414	3.3	11414	3.3	10169	2.7	10169	2.7	6665	2.3	6665	2.3
Productive	327600	94.0	326112	93.6	355740	95.4	354355	95.0	281129	94.9	279632	94.4
filter out	1744	0.5	9103	2.6	1495	0.4	7490	2.0	1381	0.5	8980	3.0
CDR3 landmarks C-F	325771	93.5	324289	93.0	354103	95.0	352725	94.6	279885	94.5	278396	94.0
filter out	1829	0.5	1823	0.5	1637	0.4	1630	0.4	1244	0.4	1236	0.4
Identity >= 95.0%	323109	92.7	321692	92.3	351084	94.2	349736	93.8	277287	93.7	275844	93.2
filter out	2662	0.8	2597	0.7	3019	0.8	2989	0.8	2598	0.9	2552	0.9
Total filter out	25420	7.3	26837	7.7	21730	5.8	23078	6.2	18801	6.3	20244	6.8
Total filter in	323109	92.7	321692	92.3	351084	94.2	349736	93.8	277287	93.7	275844	93.2
Number of Clonotypes	22743		22392		14359		14190		34304		33938
Dominant Clonotype	TRBV4-1 CASSTTGTVDEKLFF		TRBV4-1 CASSTTGTVDEKLFF		TRBV4-1 CASSTTGTVDEKLFF		TRBV4-1 CASSTTGTVDEKLFF		TRBV28 CASSPPDTGELFF		TRBV28 CASSPPDTGELFF
Dominant Clonotype Freq.		8.5		8.5093		14.8		14.8632		23.1		23.1

ISSN: 1471-2105