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==Procedures== *Sample 1M reads from raw reads and failed-to-align reads for both Ecoli SAG Illumina (101123_HL083_s4_Ecoli_IllLib) and Nextera(110120_HL087_s4_Ecoli_NexLib) sequencing data. **Using the new perl script: fastq-data-sampler-v2-hc samchiang@genemapster:~/Scripts$ perl fastq-data-sampler-v2-hc /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-PE/s_4_1and2_ID2.txt /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-PE/s_4_1and2_ID2.1Mreads 1000000 & *Deposit the sampled 10,000 reads(fastq) into galaxy server. **Use the workflow "Failed2align_1m_reads_analysis_new-v3-042311" to #Original 1M reads to construct boxplot using quality score #Random sampling 10,000 reads, extracted as fasta file. #Random sampling 1,000 reads, extracted as fasta file. *Perform the blastn (against nt database) using the sampled 10,000 and 1,000 reads (fasta format). *Using MEGAN to parse blastn results and draw the pie-chart. *Using MEGAN "compare" function is easier to interpret all of the results generated. #Import all of the .rma files (MEGAN output format)for comparison #Use normalized count setting. #Select the most specific node on taxa rank for plotting. #Plot the result in stacked bar chart and present in % ratio.
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