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===Test2: bowtie mapping to gigantic reference genome=== *Whole genome de novo assembly by ABYSS -> BLASTN contigs -> MEGAN extraction of E.coli contigs -> Joint E.coli contigs with E.coli reference genome -> build up gigantic reference genome -> map the raw reads to gigantic reference genome to count the failed-to-align reads *Started from whole genome ABYSS-pe assembly 100up data (by Chris) **ID1_Ecoli.abyss.pe.K27.contigs.100up ~ ID8_Ecoli.abyss.pe.K27.contigs.100up *BLASTN the contigs and extract E.coli contigs by MEGAN *Cat the E.coli reference genome with the MEGAN extracted E.coli contigs samchiang@genemapster:/media/disk-1/samchiang/Sub_tests_folder_imp/3_Quantify_lowquality_reads_Ecoli_SAGs/Step2_Megan_output/MEGAN output$ cat e_coli_k12_mg1655.fasta ID8_Ecoli_contigs_100up_including_summarized.new > Ecoli_gigentic_ID8 & *Build up bowtie gigantic E.coli genome samchiang@genemapster:~/Tools/bowtie-0.12.5$ ./bowtie-build /media/disk-1/samchiang/Sub_tests_folder_imp/3_Quantify_lowquality_reads_Ecoli_SAGs/Step2_Megan_output/MEGAN_output/Ecoli_gigentic_ID2 indexes/Ecoli_gigentic_index_ID2/Ecoli_gigentic_index_ID2 & *Map the raw reads to Ecoli_gigantic_index samchiang@genemapster:~/Scripts$ perl bowtie_gigantic_ID1_map /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-PE/s_4_1and2_ID1.txt /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-PE/s_4_1and2_ID1.failed.gig /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-PE/s_4_1and2_ID1.nonunique.gig &
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