Noi/NOTES/2012-2-17

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Link to calendar:[[1]]

ASM analysis of Penn data set (Batch1)[edit]

  • Link to related lab note: [[2]] [[3]]

Sample labeling[edit]

LabID Well ID Indx LabID Well ID Indx
CAPB016 A01 IndX1 KEBR007A A04 IndX25
CAPB046 B01 IndX2 KEBR028A B04 IndX26
CAPB056a C01 IndX3 KEBR042B C04 IndX27
CAPL056 D01 IndX4 KEBR040A D04 IndX28
CAPM007 E01 IndX5 KEBR061A E04 IndX29
TZHZ018A F01 IndX6 KEPK003A F04 IndX30
TZHZ033B G01 IndX7 KEPK006A G04 IndX31
TZHZ075A H01 IndX8 KEPK007A H04 IndX32
TZHZ214 A02 IndX9 KEPK010A A05 IndX33
TZHZ221B B02 IndX10 KEPK016A B05 IndX34
TZSW067 C02 IndX11 CAPM047 C05 IndX35
TZSW128B D02 IndX12 CAPM003A D05 IndX36
TZSW131A E02 IndX13 CAPM004A E05 IndX37
TZSW132B F02 IndX14 CAPM056A F05 IndX38
TZSW135B G02 IndX15 ETAM042 G05 IndX39
CAMF013A H02 IndX16 ETAM071 H05 IndX40
CAFU043 A03 IndX17 ETAM077 A06 IndX41
CAFU042 B03 IndX18 ETAM058 B06 IndX42
CAFU028 C03 IndX19 ETAM065 C06 IndX43
CAMF022A D03 IndX20 ETSB008 D06 IndX44
CAPB043 E03 IndX21 ETSB027 E06 IndX45
CAPL049 F03 IndX22 ETSB031 F06 IndX46
CAPM001A G03 IndX23 ETSB035 G06 IndX47
CAPL036 H03 IndX24 ETSB036 H06 IndX48


  • Merged and trimmed .fastq files, read1 and read2 (PE 100 read, trimmed 27 bp from 5' end) were already stored in: /home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx1_*	> 	CAPB016/PennAfrican_Batch1_Indx1.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx2_*	> 	CAPB046/PennAfrican_Batch1_Indx2.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx3_*	> 	CAPB056a/PennAfrican_Batch1_Indx3.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx4_*	> 	CAPL056/PennAfrican_Batch1_Indx4.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx5_*	> 	CAPM007/PennAfrican_Batch1_Indx5.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx6_*	> 	TZHZ018A/PennAfrican_Batch1_Indx6.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx7_*	> 	TZHZ033B/PennAfrican_Batch1_Indx7.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx8_*	> 	TZHZ075A/PennAfrican_Batch1_Indx8.fastq	
less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx9_*	> 	TZHZ214/PennAfrican_Batch1_Indx9.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx11_*	> 	TZSW067/PennAfrican_Batch1_Indx11.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx12_*	> 	TZSW128B/PennAfrican_Batch1_Indx12.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx13_*	> 	TZSW131A/PennAfrican_Batch1_Indx13.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx14_*	> 	TZSW132B/PennAfrican_Batch1_Indx14.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx15_*	> 	TZSW135B/PennAfrican_Batch1_Indx15.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx16_*	> 	CAMF013A/PennAfrican_Batch1_Indx16.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx17_*	> 	CAFU043/PennAfrican_Batch1_Indx17.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx18_*	> 	CAFU042/PennAfrican_Batch1_Indx18.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx19_*	> 	CAFU028/PennAfrican_Batch1_Indx19.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx20_*	> 	CAMF022A/PennAfrican_Batch1_Indx20.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx21_*	> 	CAPB043/PennAfrican_Batch1_Indx21.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx22_*	> 	CAPL049/PennAfrican_Batch1_Indx22.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx23_*	> 	CAPM001A/PennAfrican_Batch1_Indx23.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx24_*	> 	CAPL036/PennAfrican_Batch1_Indx24.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx25_*	> 	KEBR007A/PennAfrican_Batch1_Indx25.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx26_*	> 	KEBR028A/PennAfrican_Batch1_Indx26.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx27_*	> 	KEBR042B/PennAfrican_Batch1_Indx27.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx28_*	> 	KEBR040A/PennAfrican_Batch1_Indx28.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx29_*	> 	KEBR061A/PennAfrican_Batch1_Indx29.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx30_*	> 	KEPK003A/PennAfrican_Batch1_Indx30.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx31_*	> 	KEPK006A/PennAfrican_Batch1_Indx31.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx32_*	> 	KEPK007A/PennAfrican_Batch1_Indx32.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx33_*	> 	KEPK010A/PennAfrican_Batch1_Indx33.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx34_*	> 	KEPK016A/PennAfrican_Batch1_Indx34.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx35_*	> 	CAPM047/PennAfrican_Batch1_Indx35.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx36_*	> 	CAPM003A/PennAfrican_Batch1_Indx36.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx37_*	> 	CAPM004A/PennAfrican_Batch1_Indx37.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx38_*	> 	CAPM056A/PennAfrican_Batch1_Indx38.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx39_*	> 	ETAM042/PennAfrican_Batch1_Indx39.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx40_*	> 	ETAM071/PennAfrican_Batch1_Indx40.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx41_*	> 	ETAM077/PennAfrican_Batch1_Indx41.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx42_*	> 	ETAM058/PennAfrican_Batch1_Indx42.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx43_*	> 	ETAM065/PennAfrican_Batch1_Indx43.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx44_*	> 	ETSB008/PennAfrican_Batch1_Indx44.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx45_*	> 	ETSB027/PennAfrican_Batch1_Indx45.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx46_*	> 	ETSB031/PennAfrican_Batch1_Indx46.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx47_*	> 	ETSB035/PennAfrican_Batch1_Indx47.fastq	
#less	/home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx48_*	> 	ETSB036/PennAfrican_Batch1_Indx48.fastq
  • There is some problem with PennAfrican_Batch1_Indx8_2.txt data since I can not unzip the file (it showed "gzip: PennAfrican_Batch1_Indx8_2.txt.gz: unexpected end of file" message after I tried to unzip the data to see the problem of this data)
  • Then I used less command to print out the data in this file and count # of line, I got different number of # of line between PennAfrican_Batch1_Indx8_1.txt and PennAfrican_Batch1_Indx8_2.txt
    • PennAfrican_Batch1_Indx8_1.txt: 41,941,796
    • PennAfrican_Batch1_Indx8_2.txt: 40,285,277
  • This suggests I can not print out the whole file of PennAfrican_Batch1_Indx8_2.txt