Pacbio Data

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Contents [hide]
1 Dataset1 1.1 All Data 1.2 Randomly Selected Four SMRT cells 1.2.1 First Set 1.2.2 Second Set 1.2.3 Third Set 1.3 Randomly Selected Six SMRT cells 1.3.1 First Set 1.3.2 Second Set 1.3.3 Third Set 2 Dataset2 3 Dataset3 3.1 Randomly Selected Four SMRT cell 3.1.1 First Set 3.1.2 Second Set 3.1.3 Third Set 4 Dataset4

Dataset1

All Data

The eight SMRT cells of Ecoli MG1655 were downloaded from HGAP. We used all SMRT cells and randomly selected four and six SMRT cells three times for each in our study.

m121023_202553_42178_c100389662550000001523034410251200_s1_p0.bas.h5
m121023_224605_42178_c100389662550000001523034410251201_s1_p0.bas.h5
m121024_010654_42178_c100389662550000001523034410251202_s1_p0.bas.h5
m121024_032737_42178_c100389662550000001523034410251203_s1_p0.bas.h5
m121024_074656_42178_c100389662550000001523034410251204_s1_p0.bas.h5
m121024_100442_42178_c100389662550000001523034410251205_s1_p0.bas.h5
m121024_122509_42178_c100389662550000001523034410251206_s1_p0.bas.h5
m121024_144608_42178_c100389662550000001523034410251207_s1_p0.bas.h5

We have run smrtpipe.py (SMRT analysis) with the following params.xml to get filtered subreads of continuous long reads (CLR).

 <param name="minLength">
   <value>50</value>
 </param>
 <param name="readScore">
   <value>0.75</value>
 </param>
 <param name="minSubReadLength">
   <value>50</value>

Randomly Selected Four SMRT cells

First Set

m121024_100442_42178_c100389662550000001523034410251205_s1_p0
m121024_122509_42178_c100389662550000001523034410251206_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0

Second Set

m121024_122509_42178_c100389662550000001523034410251206_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Third Set

m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0
m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121024_074656_42178_c100389662550000001523034410251204_s1_p0

Randomly Selected Six SMRT cells

First Set

m121024_100442_42178_c100389662550000001523034410251205_s1_p0
m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_074656_42178_c100389662550000001523034410251204_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Second Set

m121024_074656_42178_c100389662550000001523034410251204_s1_p0
m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0
m121024_100442_42178_c100389662550000001523034410251205_s1_p0

Third Set

m121023_224605_42178_c100389662550000001523034410251201_s1_p0
m121023_202553_42178_c100389662550000001523034410251200_s1_p0
m121024_032737_42178_c100389662550000001523034410251203_s1_p0
m121024_122509_42178_c100389662550000001523034410251206_s1_p0
m121024_010654_42178_c100389662550000001523034410251202_s1_p0
m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Dataset2

Th four SMRT cells of Mruber were downloaded from HGAP.

m120803_022519_42141_c100388772550000001523034210251234_s1_p0.bas.h5
m120803_041200_42141_c100388772550000001523034210251235_s1_p0.bas.h5
m120803_055858_42141_c100388772550000001523034210251236_s1_p0.bas.h5
m120803_074648_42141_c100388772550000001523034210251237_s1_p0.bas.h5

Dataset3

The seven SMRT cells of Phep were downloaded from HGAP. We used all SMRT cells and randomly selected four SMRT cells three times for each in our study.
m120802_210418_42142_c100388622550000001523034210251211_s1_p0.bas.h5
m120802_225401_42142_c100388622550000001523034210251212_s1_p0.bas.h5
m120803_004251_42142_c100388622550000001523034210251213_s1_p0.bas.h5
m120803_023226_42142_c100388622550000001523034210251214_s1_p0.bas.h5
m120803_041958_42142_c100388622550000001523034210251215_s1_p0.bas.h5
m120803_060809_42142_c100388622550000001523034210251216_s1_p0.bas.h5
m120803_075818_42142_c100388622550000001523034210251217_s1_p0.bas.h5

Randomly Selected Four SMRT cell

First Set

m120802_225401_42142_c100388622550000001523034210251212_s1_p0
m120803_060809_42142_c100388622550000001523034210251216_s1_p0
m120803_004251_42142_c100388622550000001523034210251213_s1_p0
m120802_210418_42142_c100388622550000001523034210251211_s1_p0

Second Set

m120803_023226_42142_c100388622550000001523034210251214_s1_p0
m120803_075818_42142_c100388622550000001523034210251217_s1_p0
m120802_210418_42142_c100388622550000001523034210251211_s1_p0
m120803_060809_42142_c100388622550000001523034210251216_s1_p0

Third Set

m120803_041958_42142_c100388622550000001523034210251215_s1_p0
m120803_075818_42142_c100388622550000001523034210251217_s1_p0
m120803_023226_42142_c100388622550000001523034210251214_s1_p0
m120802_210418_42142_c100388622550000001523034210251211_s1_p0

Dataset4

The 17 SMRT cells of Ecoli MG 1655 were downloaded from NCBI SRA, as described in Data.