Hi all,
I am studying plasmids metagenome from clinical samples. The plasmids were captured from metagenomic DNA by digestion of linear DNA (leaving closed circular DNA safe), random insertion of transposon, and cloning into E. coli. Then, I used the purified plasmids from E. coli clones to construct the sequencing library. My plan next is to assemble the paired end reads generated from the sequencing. Now, I am expecting that the reads will have high amount of transposon and E. coli sequences that were introduced during the plasmid isolation. My question is, what is the best way to filter out reads that belong to the transposon and E. coli, leaving only transposon and E. coli FREE reads for the the assembly step? I think these sequences will highly affect the assembly process. I tried Bowtie 2.0, but it doesn't seem to be doing a good job since most of the scaffolds that I got after the de novo assembly belong to the cloning strain.
Platform is Illumina HiSeq2500 (reads are 2x150bp)
the assembler is SOAPdenovo
I hope someone could help me in this matter.
Cheers,
TJ
I am studying plasmids metagenome from clinical samples. The plasmids were captured from metagenomic DNA by digestion of linear DNA (leaving closed circular DNA safe), random insertion of transposon, and cloning into E. coli. Then, I used the purified plasmids from E. coli clones to construct the sequencing library. My plan next is to assemble the paired end reads generated from the sequencing. Now, I am expecting that the reads will have high amount of transposon and E. coli sequences that were introduced during the plasmid isolation. My question is, what is the best way to filter out reads that belong to the transposon and E. coli, leaving only transposon and E. coli FREE reads for the the assembly step? I think these sequences will highly affect the assembly process. I tried Bowtie 2.0, but it doesn't seem to be doing a good job since most of the scaffolds that I got after the de novo assembly belong to the cloning strain.
Platform is Illumina HiSeq2500 (reads are 2x150bp)
the assembler is SOAPdenovo
I hope someone could help me in this matter.
Cheers,
TJ
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