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===Test1: BLATing all failed-to-align reads=== *BLAT failed-to-align reads to E.coli genome -> output in BLAST-output format -> MEGAN extraction of E.coli reads and get quantitative information. *Since the failed-to-aling reads (e.g. s_4_ID1.failed) are FASTQ file, I need to trasform them to FASTA files before I can BLAT them. **Using script fastq2fasta-hc.pl to transfer FASTQ format to FASTA format BLAT command: samchiang@genemapster:~/Tools/blatSuite34_64$ ./blat -out=blast /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-SE/failed-or-nonspecific/s_4_ID1.failed.fa /media/disk-2/samchiang/Tools/bowtie-0.12.5/genomes/e_coli_k12_mg1655.fasta /media/disk-1/samchiang/Sub_tests_folder_imp/3_Quantify_lowquality_reads_Ecoli_SAGs/HL083_Ecoli_SAG_ID1.failed.fa.BLAT.txt & *Results **It is unclear why but The BLAT result (in BLAST output format) doesn't contain any header-string information. So MEGAN can't identify taxonomic information from BLAT results. **I did several tests and confirm that it's not due to the output format (blast or .psl) I chose. It's probably due to that the reference genome is a one string FASTA file.
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