Hi,
I enriched DNA targets by PCR, them concatenated (ligated) the DNA and sheared it to get ~300 bp sequences.
The problem is that each read may include sequences from two different genomic regions.
The sequencing was performed with HiSeq PE x 100.
How can I do the alignment with free software?
In regular enrichments (RNA hybridization) I'm just using bwa and samtools, but I don't know if it is suitable for this case as well?
Thanks,
Lilach
I enriched DNA targets by PCR, them concatenated (ligated) the DNA and sheared it to get ~300 bp sequences.
The problem is that each read may include sequences from two different genomic regions.
The sequencing was performed with HiSeq PE x 100.
How can I do the alignment with free software?
In regular enrichments (RNA hybridization) I'm just using bwa and samtools, but I don't know if it is suitable for this case as well?
Thanks,
Lilach
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