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@drio
drio / old_pe
Created April 30, 2010 22:23
pe solid data
LOG: Processing arguments
LOG: Parsing options
LOG: Start at 2010-04-30T17:22:25-05:00
LOG: action = sea_create
LOG: c_design = /users/p-solid/ccds
LOG: run_name = 0097_20100115_2_SP_AWG_HCC_L09_0112_T_000sA_01003280874_1
LOG: Loading action: /stornext/snfs1/next-gen/drio-scratch/working.copies/hgsc.bfast.pipe/lib/d_actions/sea_remove
LOG: Loading action: /stornext/snfs1/next-gen/drio-scratch/working.copies/hgsc.bfast.pipe/lib/d_actions/sea_create
LOG: Instanciating Action: sea_create
LOG: Checking if SEA is already there ...
@drio
drio / gist:389935
Created May 4, 2010 20:35
dnaa
5270
25
1 0 0 299 5270
2 0 0 274 5270
3 0 0 265 5270
4 0 0 314 5270
5 0 0 297 5269
6 0 0 271 5270
7 0 0 289 5270
8 0 0 311 5270
@drio
drio / dnaa
Created May 4, 2010 20:39
dnaa
5182
25
1 0 0 206 5182
2 0 0 247 5180
3 0 0 272 5179
4 0 0 275 5180
5 0 0 267 5180
6 0 0 316 5181
7 0 0 285 5182
8 0 0 308 5182
@drio
drio / gist:389944
Created May 4, 2010 20:40
r
R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
@drio
drio / gist:390916
Created May 5, 2010 15:22
gplot gnuplot errorrate erate
#!/bin/bash
sample="test"
data_f="/tmp/data.txt"
gp_cfg_f="/tmp/gplot.${sample}.cfg"
input_file=$1
#1 220 5220
#2 252 5215
@drio
drio / gist:390923
Created May 5, 2010 15:25
gplot error gnuplot
#!/bin/bash
#
# ./dqc postalignqc -f bf.indexes/ecoli.drio.test.fa \
# -r 0:2000 /Users/drio/projects/synthetic.pipe/bf.bwt.sorted.bam > /tmp/foo.txt
# R CMD BATCH '--args in.file="/tmp/foo.txt" out.type="png" space="0" expid="test"' plot_dqc_postalignqc.R
#
sample="test"
data_f="/tmp/data.txt"
gp_cfg_f="/tmp/gplot.${sample}.cfg"
@drio
drio / gist:390952
Created May 5, 2010 15:36
#!/bin/bash
#
# ./dqc postalignqc -f bf.indexes/ecoli.drio.test.fa \
# -r 0:2000 /Users/drio/projects/synthetic.pipe/bf.bwt.sorted.bam > /tmp/foo.txt
# R CMD BATCH '--args in.file="/tmp/foo.txt" out.type="png" space="0" expid="test"' plot_dqc_postalignqc.R
#
sample="test"
data_f="/tmp/data.txt"
gp_cfg_f="/tmp/gplot.${sample}.cfg"
@drio
drio / gist:390955
Created May 5, 2010 15:36
Chr1_2359_1902_1_1_0:0:0_2:0:0_137 16 Chr1 2359 255 25M * 0 0 TCTGGTATGGATGTGGCGCGTAAAC +???????????????????????? PG:Z:bfast AS:i:1250 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:25 CS:Z:A2100313333011132013310122 CQ:Z:+++++++++++++++++++++++++ CM:i:0 XA:i:3 XE:Z:-------------------------
Chr1_2986_3502_0_0_1:0:0_2:0:0_ac3 0 Chr1 2986 255 25M * 0 0 AAATATCGTTTATCAGTGCTGGGAG ??????????????""????????+ PG:Z:bfast AS:i:1125 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:25 CS:Z:A0003332310033210113210022 CQ:Z:+++++++++++++++++++++++++ CM:i:1 XA:i:3 XE:Z:---------------0---------
Chr1_3317_2809_1_1_2:0:0_0:0:0_29 16 Chr1 3317 255 25M * 0 0 TGGGTGCTGGCGTATCCGGGGATTA +????""????""???????????? PG:Z:bfast AS:i:1000 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:25 CS:Z:A3303200030233333012211001 CQ:Z:+++++++++++++++++++++++++ CM:i:2 XA:i:3 XE:Z:-----2-----3-------------
Chr1_6954_6365_1_1_0:0:0_3:0:0_1e22 16 Chr1 6954 255 25M * 0 0 TAAGCTGAATACCTTCCAGCGGCAT +???????????????????????? PG:Z:bfast AS:i:1250 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:25 CS:Z:A03130332102
@drio
drio / gist:390956
Created May 5, 2010 15:37
@HD VN:0.1.2 SO:unsorted GO:none
@SQ SN:Chr1 LN:4639675
@PG ID:bfast VN:0.6.4c
Chr1_2359_1902_1_1_0:0:0_2:0:0_137 16 Chr1 2359 255 25M * 0 0 TCTGGTATGGATGTGGCGCGTAAAC +???????????????????????? PG:Z:bfast AS:i:1250 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:25 CS:Z:A2100313333011132013310122 CQ:Z:+++++++++++++++++++++++++ CM:i:0 XA:i:3 XE:Z:-------------------------
Chr1_2986_3502_0_0_1:0:0_2:0:0_ac3 0 Chr1 2986 255 25M * 0 0 AAATATCGTTTATCAGTGCTGGGAG ??????????????""????????+ PG:Z:bfast AS:i:1125 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:25 CS:Z:A0003332310033210113210022 CQ:Z:+++++++++++++++++++++++++ CM:i:1 XA:i:3 XE:Z:---------------0---------
Chr1_3317_2809_1_1_2:0:0_0:0:0_29 16 Chr1 3317 255 25M * 0 0 TGGGTGCTGGCGTATCCGGGGATTA +????""????""???????????? PG:Z:bfast AS:i:1000 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:25 CS:Z:A3303200030233333012211001 CQ:Z:+++++++++++++++++++++++++ CM:i:2 XA:i:3 XE:Z:-----2-----3-------------
Chr1_6954_6365_1_1_0:0:0_3:0:0_1e22 16 Chr1 6954 255 25M * 0 0 TAAGCTGAATACCTTCCAGCGGCAT +????????????????????
@drio
drio / gist:391379
Created May 5, 2010 20:29
#!/bin/bash
#
# /stornext/snfs1/next-gen/drio-scratch/bfast_related/dnaa/dqc postalignqc -f
# -f /stornext/snfs4/next-gen/solid/bf.references/h/hsap.36.1.hg18/hsap_36.1_hg18.fa
# -r 0:2000 /Users/drio/projects/synthetic.pipe/bf.bwt.sorted.bam > /tmp/foo.txt
# R CMD BATCH '--args in.file="/tmp/foo.txt" out.type="png" space="0" expid="test"' plot_dqc_postalignqc.R
#
sample="test"
data_f="/tmp/data.txt"
gp_cfg_f="/tmp/gplot.${sample}.cfg"