added configs

Author: Piotr Balwierz

badU20MmSamples.txt

@@ -0,0 +1,24 @@
+CNhs11572	8	1000	10
+CNhs12521	8	200	10
+CNhs12770	10	200	20
+CNhs12784	10	1000	200
+CNhs13409	8	180	20
+CNhs14143	6	100	2
+CNhs14144	3	60	9
+CNhs14146	5	100	30
+CNhs14147	5	70	10
+CNhs14149	6	150	30
+CNhs14150	10	200	50
+CNhs14162	5	30	50
+CNhs14163	5	200	30
+CNhs14332	5	200	20
+CNhs14338	5	100	10
+CNhs14339	5	100	10
+CNhs14340	10	100	10
+CNhs14341	5	100	50
+CNhs14372	5	50	30
+CNhs14374	10	200	50
+CNhs14375	5	50	5
+CNhs14402	6	100	20
+CNhs14403	5	200	10
+CNhs14521	6	50	20

badU21HsSamples.txt

@@ -0,0 +1,84 @@
+CNhs12458	20	1000	100
+CNhs12459	25	1000	100
+CNhs12460	25	1000	100
+CNhs12461	25	1000	100
+CNhs12462	25	1000	100
+CNhs12463	25	1000	100
+CNhs12464	25	1000	100
+CNhs12465	25	1000	100
+CNhs12466	25	1000	100
+CNhs12467	25	1000	100
+CNhs12468	25	1000	100
+CNhs12469	25	1000	100
+CNhs12470	25	1000	100
+CNhs12471	25	1000	100
+CNhs12472	25	1000	100
+CNhs12473	25	1000	100
+CNhs12474	25	1000	100
+#CNhs12684	strange slope
+CNhs12687	20	1000	50
+CNhs12688	20	1000	50
+CNhs12689	20	1000	50
+CNhs12698	20	1000	50
+CNhs12699	20	1000	50
+CNhs12700	20	1000	50
+CNhs12701	20	1000	50
+CNhs12702	20	1000	50
+CNhs12787	10	1000	20
+CNhs12788	20	1000	50
+CNhs12789	20	1000	50
+CNhs12790	20	1000	50
+CNhs12791	20	1000	50
+CNhs12792	20	1000	50
+CNhs12793	20	1000	50
+CNhs12794	20	1000	50
+CNhs12795	20	1000	50
+CNhs12796	20	1000	50
+CNhs12797	20	1000	50
+CNhs12798	20	1000	50
+CNhs12799	20	1000	50
+CNhs12800	20	1000	50
+CNhs12801	20	1000	50
+CNhs12802	20	1000	50
+CNhs12803	20	1000	50
+CNhs12804	20	1000	50
+#CNhs11163 - little tags
+#CNhs11164 - little tags
+CNhs11785	6	60	50
+CNhs11793	8	100	50
+CNhs12128	8	200	90
+CNhs12192	7	160	60
+CNhs12195	10	100	70
+# In the region CNhs12469 + bending up
+# (good but huge CNhs12519)
+CNhs12522	8	100	30
+CNhs12523	5	50	100
+CNhs12524	5	50	100
+CNhs12525	10	300	50
+CNhs12526	10	100	60
+CNhs12529	10	200	50
+CNhs12530	8	80	40
+CNhs12545	8	80	60
+CNhs12547	7	60	40
+CNhs12622	6	60	30
+CNhs12623	8	80	20
+CNhs12684	10	100	100
+CNhs12690	8	90	30
+CNhs12691	8	100	80
+CNhs12692	8	100	30
+CNhs12693	8	100	50
+CNhs12694	8	100	30
+CNhs12695	8	100	30
+CNhs12696	8	100	50
+CNhs12697	8	100	30
+CNhs12786	8	500	29
+CNhs12930	8	200	10
+CNhs13147	6	70	10
+CNhs13148	8	70	20
+# CNhs13150 very little tags!
+CNhs13150	2	20	4
+CNhs13151	8	40	20
+CNhs13153	8	100	10
+CNhs13187	8	100	10
+CNhs13427	8	40	20
+CNhs13610	8	70	10

pipelineHumanFull_U22.conf

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+dir: /import/bc2/home/nimwegen/GROUP/Promoterome/PrimaryData/UPDATE_022/Human.Links/
+tmpDir: /mnt/biggles/csc_home/piotr/Work/FANTOM5/Data/ResultsHumanFull_U22/
+cumDir: Cumulatives/
+mappedDir: Mapped/
+normDir: Normalized/
+normDirSplit: NormalizedSplit/
+fitDir: Fit/
+fitRegionF: /mnt/biggles/csc_home/piotr/Work/FANTOM5/Analysis/CagePipeline/badU21HsSamples.txt

pipelineMouseFull_U22.conf

@@ -0,0 +1,11 @@
+#dir: /mnt/biggles/csc_projects/piotr/FANTOM5/Data/PrimaryData/UPDATE_023/mouse.tissue.hCAGE/ #done
+#dir: /mnt/biggles/csc_projects/piotr/FANTOM5/Data/PrimaryData/UPDATE_023/mouse.primary_cell.hCAGE/  #done
+#dir: /mnt/biggles/csc_projects/piotr/FANTOM5/Data/PrimaryData/UPDATE_023/mouse.qualitycontrol.hCAGE/ #done
+dir: /mnt/biggles/csc_projects/piotr/FANTOM5/Data/PrimaryData/UPDATE_023/mouse.timecourse.hCAGE/ 
+tmpDir: /mnt/biggles/csc_home/piotr/Work/FANTOM5/Data/ResultsMouseFull_U22/
+cumDir: Cumulatives/
+mappedDir: Mapped/
+normDir: Normalized/
+normDirSplit: NormalizedSplit/
+fitDir: Fit/
+fitRegionF: /mnt/biggles/csc_home/piotr/Work/FANTOM5/Analysis/CagePipeline/badU20MmSamples.txt

pipelineMouseRattic_U23.conf

@@ -0,0 +1,9 @@
+dir: /mnt/biggles/csc_home/piotr/Work/FANTOM5/Data/PrimaryData/UPDATE_023/Links/
+tmpDir: /mnt/biggles/csc_home/piotr/Work/FANTOM5/Data/ResultsMouseRattic_U23/
+cumDir: Cumulatives/
+mappedDir: Mapped/
+normDir: Normalized/
+normDirSplit: NormalizedSplit/
+fitDir: Fit/
+fitRegionF: /dev/null
+# /mnt/biggles/csc_home/piotr/Work/FANTOM5/Analysis/CagePipeline/badU20MmSamples.txt