Pacbio Data

Revision as of 31 October 2013 02:52 by admin (Comments | Contribs) | (→Randomly Selected four SMRT cell)
Contents

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

Random Get @m121024_100442_42178_c100389662550000001523034410251205_s1_p0
Random Get @m121024_122509_42178_c100389662550000001523034410251206_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0

Second Set

Random Get @m121024_122509_42178_c100389662550000001523034410251206_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Third Set

Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0
Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121024_074656_42178_c100389662550000001523034410251204_s1_p0

Randomly Selected Six SMRT cells

First Set

Random Get @m121024_100442_42178_c100389662550000001523034410251205_s1_p0
Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_074656_42178_c100389662550000001523034410251204_s1_p0
Random Get @m121024_144608_42178_c100389662550000001523034410251207_s1_p0

Second Set

Random Get @m121024_074656_42178_c100389662550000001523034410251204_s1_p0
Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_144608_42178_c100389662550000001523034410251207_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0
Random Get @m121024_100442_42178_c100389662550000001523034410251205_s1_p0

Third Set

Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_122509_42178_c100389662550000001523034410251206_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0
Random Get @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.

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

Random Get @m120802_225401_42142_c100388622550000001523034210251212_s1_p0 Random Get @m120803_060809_42142_c100388622550000001523034210251216_s1_p0 Random Get @m120803_004251_42142_c100388622550000001523034210251213_s1_p0 Random Get @m120802_210418_42142_c100388622550000001523034210251211_s1_p0

Second set

Random Get @m120803_023226_42142_c100388622550000001523034210251214_s1_p0 Random Get @m120803_075818_42142_c100388622550000001523034210251217_s1_p0 Random Get @m120802_210418_42142_c100388622550000001523034210251211_s1_p0 Random Get @m120803_060809_42142_c100388622550000001523034210251216_s1_p0

Third set

Random Get @m120803_041958_42142_c100388622550000001523034210251215_s1_p0 Random Get @m120803_075818_42142_c100388622550000001523034210251217_s1_p0 Random Get @m120803_023226_42142_c100388622550000001523034210251214_s1_p0 Random Get @m120802_210418_42142_c100388622550000001523034210251211_s1_p0

Dataset4

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