annotate test-data/test3.chimjunc.tabular @ 12:79b885ce78d7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb

chr_donorA	brkpt_donorA	strand_donorA	chr_acceptorB	brkpt_acceptorB	strand_acceptorB	junction_type	repeat_left_lenA	repeat_right_lenB	read_name	start_alnA	cigar_alnA	start_alnB	cigar_alnB	num_chim_aln	max_poss_aln_score	non_chim_aln_score	this_chim_aln_score	bestall_chim_aln_score	PEmerged_bool	readgrp
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_60	181	60M15S	241	60S15M	1	75	59	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_62	183	58M17S	241	58S17M	1	75	57	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_64	185	56M19S	241	56S19M	1	75	55	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_66	187	54M21S	241	54S21M	1	75	53	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_68	189	52M23S	241	52S23M	1	75	51	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_70	191	50M25S	241	50S25M	1	75	49	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_72	193	48M27S	241	48S27M	1	75	47	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_74	195	46M29S	241	46S29M	1	75	45	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_76	197	44M31S	241	44S31M	1	75	43	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_78	199	42M33S	241	42S33M	1	75	41	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_80	201	40M35S	241	40S35M	1	75	39	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_82	203	38M37S	241	38S37M	1	75	37	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_84	205	36M39S	241	36S39M	1	75	38	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_86	207	34M41S	241	34S41M	1	75	40	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_88	209	32M43S	241	32S43M	1	75	42	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_90	211	30M45S	241	30S45M	1	75	44	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_92	213	28M47S	241	28S47M	1	75	46	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_94	215	26M49S	241	26S49M	1	75	48	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_96	217	24M51S	241	24S51M	1	75	50	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_98	219	22M53S	241	22S53M	1	75	52	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_100	221	20M55S	241	20S55M	1	75	54	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_102	223	18M57S	241	18S57M	1	75	56	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_104	225	16M59S	241	16S59M	1	75	58	72	72	0
chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_106	227	14M61S	241	14S61M	1	75	60	72	72	0
# 2.7.2a   STAR --runThreadN 1 --genomeLoad NoSharedMemory --genomeDir tempstargenomedir @ --readFilesIn /tmp/tmpTNNe38/files/2/7/0/dataset_2700161e-e03d-4a50-9bc8-1508ff059881.dat --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --twopassMode None  --quantMode - --outSAMstrandField intronMotif --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM NM MD jM jI MC ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 255 --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --outBAMsortingThreadN 1 --outBAMsortingBinsN 50 --limitBAMsortRAM 0 --chimOutType Junctions --chimOutJunctionFormat 1
# Nreads 83	NreadsUnique 72	NreadsMulti 0