Commits

David Gomez-Cabrero committed cec9db9

Example II

Comments (0)

Files changed (30)

Example/Necessary_Files/K562_chr20_21.bam

Binary file added.

Example/Outputs_pdfs/K562Example_BIASES.pdf

Binary file added.

Example/Outputs_pdfs/K562Example_CHRO.pdf

Binary file added.

Example/Outputs_pdfs/K562Example_report_RE_distances.pdf

Binary file added.

Example/Outputs_pdfs/K562Example_report_distances_CYS.pdf

Binary file added.

Example/Outputs_text_files/K562Example_GC_cys.txt

+138.0	159.0	150.0	135.0	167.0	264.0	66.0	280.0	157.0	69.0	244.0	78.0	283.0	176.0	158.0	329.0	201.0	113.0	287.0	162.0
+159.0	170.0	172.0	166.0	174.0	255.0	50.0	263.0	184.0	61.0	271.0	92.0	304.0	229.0	155.0	345.0	246.0	149.0	351.0	205.0
+150.0	172.0	196.0	189.0	182.0	320.0	72.0	312.0	201.0	74.0	323.0	99.0	316.0	242.0	184.0	424.0	262.0	167.0	384.0	271.0
+135.0	166.0	189.0	180.0	174.0	259.0	60.0	280.0	191.0	75.0	278.0	84.0	324.0	235.0	183.0	433.0	259.0	139.0	392.0	254.0
+167.0	174.0	182.0	174.0	202.0	275.0	75.0	318.0	191.0	89.0	346.0	84.0	352.0	250.0	188.0	459.0	292.0	186.0	438.0	322.0
+264.0	255.0	320.0	259.0	275.0	392.0	118.0	507.0	329.0	134.0	523.0	148.0	553.0	394.0	299.0	758.0	501.0	279.0	649.0	441.0
+66.0	50.0	72.0	60.0	75.0	118.0	20.0	132.0	90.0	28.0	132.0	44.0	156.0	100.0	89.0	219.0	127.0	68.0	189.0	128.0
+280.0	263.0	312.0	280.0	318.0	507.0	132.0	586.0	368.0	131.0	603.0	135.0	645.0	481.0	380.0	855.0	538.0	318.0	798.0	555.0
+157.0	184.0	201.0	191.0	191.0	329.0	90.0	368.0	268.0	93.0	422.0	107.0	389.0	292.0	222.0	538.0	357.0	205.0	506.0	355.0
+69.0	61.0	74.0	75.0	89.0	134.0	28.0	131.0	93.0	44.0	162.0	43.0	185.0	132.0	98.0	210.0	154.0	113.0	224.0	185.0
+244.0	271.0	323.0	278.0	346.0	523.0	132.0	603.0	422.0	162.0	666.0	166.0	744.0	487.0	427.0	960.0	551.0	395.0	944.0	644.0
+78.0	92.0	99.0	84.0	84.0	148.0	44.0	135.0	107.0	43.0	166.0	56.0	174.0	129.0	94.0	247.0	145.0	94.0	218.0	190.0
+283.0	304.0	316.0	324.0	352.0	553.0	156.0	645.0	389.0	185.0	744.0	174.0	766.0	623.0	474.0	1035.0	724.0	481.0	1085.0	783.0
+176.0	229.0	242.0	235.0	250.0	394.0	100.0	481.0	292.0	132.0	487.0	129.0	623.0	464.0	322.0	763.0	553.0	302.0	749.0	562.0
+158.0	155.0	184.0	183.0	188.0	299.0	89.0	380.0	222.0	98.0	427.0	94.0	474.0	322.0	260.0	609.0	445.0	231.0	602.0	464.0
+329.0	345.0	424.0	433.0	459.0	758.0	219.0	855.0	538.0	210.0	960.0	247.0	1035.0	763.0	609.0	1506.0	1019.0	593.0	1535.0	1242.0
+201.0	246.0	262.0	259.0	292.0	501.0	127.0	538.0	357.0	154.0	551.0	145.0	724.0	553.0	445.0	1019.0	634.0	471.0	1120.0	919.0
+113.0	149.0	167.0	139.0	186.0	279.0	68.0	318.0	205.0	113.0	395.0	94.0	481.0	302.0	231.0	593.0	471.0	308.0	641.0	564.0
+287.0	351.0	384.0	392.0	438.0	649.0	189.0	798.0	506.0	224.0	944.0	218.0	1085.0	749.0	602.0	1535.0	1120.0	641.0	1866.0	1513.0
+162.0	205.0	271.0	254.0	322.0	441.0	128.0	555.0	355.0	185.0	644.0	190.0	783.0	562.0	464.0	1242.0	919.0	564.0	1513.0	1464.0

Example/Outputs_text_files/K562Example_GC_trans.txt

+4.0	5.0	2.0	4.0	9.0	10.0	2.0	10.0	7.0	3.0	10.0	5.0	16.0	7.0	4.0	16.0	8.0	6.0	18.0	11.0
+5.0	4.0	3.0	5.0	9.0	5.0	0.0	15.0	6.0	2.0	19.0	6.0	18.0	11.0	9.0	13.0	12.0	10.0	14.0	16.0
+2.0	3.0	8.0	5.0	1.0	9.0	8.0	15.0	3.0	5.0	18.0	4.0	17.0	16.0	11.0	12.0	14.0	5.0	15.0	16.0
+4.0	5.0	5.0	4.0	10.0	12.0	8.0	13.0	10.0	4.0	13.0	6.0	13.0	15.0	13.0	18.0	9.0	13.0	21.0	13.0
+9.0	9.0	1.0	10.0	2.0	12.0	5.0	12.0	10.0	7.0	8.0	5.0	22.0	10.0	12.0	22.0	10.0	11.0	19.0	21.0
+10.0	5.0	9.0	12.0	12.0	24.0	7.0	18.0	20.0	5.0	24.0	8.0	20.0	18.0	8.0	36.0	27.0	14.0	29.0	23.0
+2.0	0.0	8.0	8.0	5.0	7.0	0.0	3.0	0.0	1.0	11.0	3.0	8.0	3.0	3.0	5.0	5.0	4.0	13.0	5.0
+10.0	15.0	15.0	13.0	12.0	18.0	3.0	28.0	7.0	5.0	26.0	5.0	24.0	14.0	13.0	36.0	33.0	19.0	26.0	30.0
+7.0	6.0	3.0	10.0	10.0	20.0	0.0	7.0	10.0	3.0	17.0	7.0	14.0	16.0	8.0	22.0	16.0	5.0	21.0	17.0
+3.0	2.0	5.0	4.0	7.0	5.0	1.0	5.0	3.0	0.0	7.0	2.0	6.0	4.0	10.0	15.0	3.0	1.0	12.0	9.0
+10.0	19.0	18.0	13.0	8.0	24.0	11.0	26.0	17.0	7.0	30.0	6.0	26.0	19.0	11.0	43.0	24.0	13.0	42.0	39.0
+5.0	6.0	4.0	6.0	5.0	8.0	3.0	5.0	7.0	2.0	6.0	0.0	7.0	6.0	5.0	8.0	5.0	0.0	13.0	7.0
+16.0	18.0	17.0	13.0	22.0	20.0	8.0	24.0	14.0	6.0	26.0	7.0	48.0	18.0	12.0	47.0	32.0	18.0	39.0	28.0
+7.0	11.0	16.0	15.0	10.0	18.0	3.0	14.0	16.0	4.0	19.0	6.0	18.0	6.0	11.0	30.0	21.0	11.0	32.0	27.0
+4.0	9.0	11.0	13.0	12.0	8.0	3.0	13.0	8.0	10.0	11.0	5.0	12.0	11.0	8.0	23.0	13.0	8.0	20.0	8.0
+16.0	13.0	12.0	18.0	22.0	36.0	5.0	36.0	22.0	15.0	43.0	8.0	47.0	30.0	23.0	52.0	36.0	32.0	43.0	52.0
+8.0	12.0	14.0	9.0	10.0	27.0	5.0	33.0	16.0	3.0	24.0	5.0	32.0	21.0	13.0	36.0	20.0	20.0	34.0	26.0
+6.0	10.0	5.0	13.0	11.0	14.0	4.0	19.0	5.0	1.0	13.0	0.0	18.0	11.0	8.0	32.0	20.0	2.0	14.0	22.0
+18.0	14.0	15.0	21.0	19.0	29.0	13.0	26.0	21.0	12.0	42.0	13.0	39.0	32.0	20.0	43.0	34.0	14.0	42.0	41.0
+11.0	16.0	16.0	13.0	21.0	23.0	5.0	30.0	17.0	9.0	39.0	7.0	28.0	27.0	8.0	52.0	26.0	22.0	41.0	38.0

Example/Outputs_text_files/K562Example_MAP_cys.txt

+2.0	2.0	2.0	2.0	329.0
+2.0	2.0	6.0	4.0	550.0
+2.0	6.0	4.0	7.0	770.0
+2.0	4.0	7.0	16.0	1172.0
+329.0	550.0	770.0	1172.0	131722.0

Example/Outputs_text_files/K562Example_MAP_trans.txt

+0.0	0.0	1.0	0.0	23.0
+0.0	0.0	0.0	1.0	33.0
+1.0	0.0	0.0	1.0	33.0
+0.0	1.0	1.0	2.0	53.0
+23.0	33.0	33.0	53.0	5324.0

Example/Outputs_text_files/K562Example_QUANTILES_GC.txt

+0.00
+26.50
+29.00
+30.00
+31.50
+32.98
+34.00
+35.00
+36.00
+37.00
+38.00
+39.00
+40.00
+41.20
+42.80
+44.00
+46.00
+48.00
+50.00
+54.00
+100.00

Example/Outputs_text_files/K562Example_QUANTILES_MAP.txt

+0.50
+0.60
+0.70
+0.80
+0.90
+1.00

Example/Outputs_text_files/K562Example_QUANTILES_fragl.txt

+6.00
+153.00
+321.00
+501.00
+698.00
+918.00
+1147.00
+1399.00
+1673.00
+1967.00
+2295.00
+2655.00
+3059.00
+3524.00
+4055.00
+4684.00
+5458.00
+6478.00
+7939.00
+10484.00
+30216690.00