Hello community.
I am new to NGS world and I'm facing some problems while trying to align my reads with a reference genome.
First, let me explain what I'm doing. I am working with a plasmid of about 44 kb that I've sequenced with Illumina MiSeq. Now, I sequenced 7 other plasmids from the same species (different strains). I used an Ion PGM for these other 7 samples.
Now, I was using bowtie2 to align my reads with the plasmid's genome that I've sequenced with the Illumina's platform and almost all the reads (from 260,000 to 360,00 depending on the sample) do not align with my reference genome.
Do you think I might be doing something wrong in this process? Or there's the possibility that I have something wrong with the sequencing (the contigs generated with the assembler plugin from Ion's platform do not align with the plasmids)?
Thank you in advance.
I am new to NGS world and I'm facing some problems while trying to align my reads with a reference genome.
First, let me explain what I'm doing. I am working with a plasmid of about 44 kb that I've sequenced with Illumina MiSeq. Now, I sequenced 7 other plasmids from the same species (different strains). I used an Ion PGM for these other 7 samples.
Now, I was using bowtie2 to align my reads with the plasmid's genome that I've sequenced with the Illumina's platform and almost all the reads (from 260,000 to 360,00 depending on the sample) do not align with my reference genome.
Do you think I might be doing something wrong in this process? Or there's the possibility that I have something wrong with the sequencing (the contigs generated with the assembler plugin from Ion's platform do not align with the plasmids)?
Thank you in advance.
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