We have sequenced metagenomic data and metatranscriptomic data by Hiseq2000 paired-end of acid mine drainage.
we run velvet to assemble the metagenomic data,and we succeeded to assemble 3 draft genomes(or bining sequences).
I would like to map the metatranscriptomic data to 3 drafts. I have tried with bowtie and soapaliner/soap2.
soap -a RNA_1.fasta -b RNA_2.fasta -D draft_geneome_ORFS_db.index -v 3 -r 2 -s 40 -m 400 -x 600 -o PE.out -2 SE.out
soap -a RNA_1.fasta -D draft_genome_ORFs_db.index -v 3 -r 2 -s 40 -o SE.out
but the results are both very poor,the mapping results are less than 1% .
while I use the total contigs of metagenomic data as reference,the mapping result can be 83%.
Does anyone know the methods to deal with my problems? Thanks a millon!
we run velvet to assemble the metagenomic data,and we succeeded to assemble 3 draft genomes(or bining sequences).
I would like to map the metatranscriptomic data to 3 drafts. I have tried with bowtie and soapaliner/soap2.
soap -a RNA_1.fasta -b RNA_2.fasta -D draft_geneome_ORFS_db.index -v 3 -r 2 -s 40 -m 400 -x 600 -o PE.out -2 SE.out
soap -a RNA_1.fasta -D draft_genome_ORFs_db.index -v 3 -r 2 -s 40 -o SE.out
but the results are both very poor,the mapping results are less than 1% .
while I use the total contigs of metagenomic data as reference,the mapping result can be 83%.
Does anyone know the methods to deal with my problems? Thanks a millon!
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