Version Differences for Dataset2

(→Short reads)
Line 9:
  Insert size ~ 300bp    Insert size ~ 300bp 
       
- We converted the required format using Picard tools ([http://picard.sourceforge.net/command-line-overview.shtml ref]).   + We combined MiSeq_Ecoli_MG1655_110721_PF_R1.fastq and MiSeq_Ecoli_MG1655_110721_PF_R2.fastq to MiSeq_PE.fastq.  
       
- java -jar SamToFastq.jar INPUT=Ecoli_MG1655_s_6_1_bfast.bam FASTQ=Ecoli_MG1655_s1.fastq   + The data in frg format were downloaded from [ftp://ftp.cbcb.umd.edu/pub/data/PBcR/closure_paper/K12/miseq.100X.frg.bz2 Miseq100X]  
- java -jar SamToFastq.jar INPUT=Ecoli_MG1655_s_6_2_bfast.bam FASTQ=Ecoli_MG1655_s2.fastq   + == 118X (HQ) ==  
    + We have trimmed the sequence reads to be of error probability less than 0.05. The paired-end reads were discarded if one read is shorter than 150bp.  
       
- We combined MiSeq_Ecoli_MG1655_110721_PF_R1.fastq and MiSeq_Ecoli_MG1655_110721_PF_R2.fastq to MiSeq_PE.fastq.   + We therefore obtained 1,839,935 paired-end reads (~118X) with high quality for further analysis.  
       
       
  java convertFastqToFastaAndQual MiSeq_PE.fastq MiSeq_PE.fna MiSeq_PE.qual    java convertFastqToFastaAndQual MiSeq_PE.fastq MiSeq_PE.fna MiSeq_PE.qual