Hi all,
I have a set of 75bp SE illumina reads.My problem is that for some samples I am able to map almost 85% of the reads,but for some the mapping percentage is very low,about 20-30% (using MAQ,bwa,bowtie).I tried using bowtie options to trim,increase the mismatches etc.,with no significant increase in mapping.I also ran fastqc on mapped and unmapped reads but it looks very similar.I blasted some of the unmapped sequences,and some seems to be rRNA genes.Is there a way to find out what exactly is different between these libraries? Can I include such samples with high mapping and low mapping as biological replicates (or as test Vs control) for differential gene expression?
Thanks!
I have a set of 75bp SE illumina reads.My problem is that for some samples I am able to map almost 85% of the reads,but for some the mapping percentage is very low,about 20-30% (using MAQ,bwa,bowtie).I tried using bowtie options to trim,increase the mismatches etc.,with no significant increase in mapping.I also ran fastqc on mapped and unmapped reads but it looks very similar.I blasted some of the unmapped sequences,and some seems to be rRNA genes.Is there a way to find out what exactly is different between these libraries? Can I include such samples with high mapping and low mapping as biological replicates (or as test Vs control) for differential gene expression?
Thanks!
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