Hi everyone,
I tried a rather ambitious experiment in which I tried barcoding several samples of human DNA using a homemade barcodes, target selecting for a few genes by microarray followed by sequencing on the illumina GAII. I used 100bp paired end reads with an index cycle. I could parse my barcodes just fine but when I tried mapping my reads, I got a very low number that mapped back to the human genome (60%) and only 25% to my targeted region. I tried using both ELAND and BWA default settings for paired end reads (actually I added the -q15 in BWA). Is there anything I can do to "salvage" this experiment? Are there different parameters in BWA and Illumina that I could try or is my read quality just that bad. What is odd is that when I look at the quality score of my reads, I don't think they are that bad so I'm confused as to why so few would map back. Any help would be greatly appreciated!!
Cheers,
Ali
I tried a rather ambitious experiment in which I tried barcoding several samples of human DNA using a homemade barcodes, target selecting for a few genes by microarray followed by sequencing on the illumina GAII. I used 100bp paired end reads with an index cycle. I could parse my barcodes just fine but when I tried mapping my reads, I got a very low number that mapped back to the human genome (60%) and only 25% to my targeted region. I tried using both ELAND and BWA default settings for paired end reads (actually I added the -q15 in BWA). Is there anything I can do to "salvage" this experiment? Are there different parameters in BWA and Illumina that I could try or is my read quality just that bad. What is odd is that when I look at the quality score of my reads, I don't think they are that bad so I'm confused as to why so few would map back. Any help would be greatly appreciated!!
Cheers,
Ali
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