Noi/NOTES/2012-2-17
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Link to calendar:[[1]]
ASM analysis of Penn data set (Batch1)[edit]
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