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Hi,
I am trying to align the human mitochondrial transcriptome reads using Bowtie and BWA, but after following the procedure in the article it fails to align accordingly to the hg18 genome (same genome as used by the authors).
It involved removal of adaptor sequences, removal of poly A tails and removal of CCA nucleotides from 3' end.
I have a few questions regarding the trimming. When i scanned the mito genome for the adaptor it was not present but the adaptor sequence is present within the reads (in the middle).
How is such a thing possible and why does only half of the reads have the adaptor sequence??
Has anyone tried aligning these reads? If so have you been able to reproduce the same results as that mentioned in the article? If so how??
I am trying to align the human mitochondrial transcriptome reads using Bowtie and BWA, but after following the procedure in the article it fails to align accordingly to the hg18 genome (same genome as used by the authors).
It involved removal of adaptor sequences, removal of poly A tails and removal of CCA nucleotides from 3' end.
I have a few questions regarding the trimming. When i scanned the mito genome for the adaptor it was not present but the adaptor sequence is present within the reads (in the middle).
How is such a thing possible and why does only half of the reads have the adaptor sequence??
Has anyone tried aligning these reads? If so have you been able to reproduce the same results as that mentioned in the article? If so how??