Hi all,
I need to analyze paired ends reads for a target re-sequencing experiment in which the repeated regions of my targets were masked.
I have performed the alignment with BWA and converted the export of BWA alignment in a SAM file. Then using SamTool I have removed duplicated reads and run the SNP and indel calling. Does anyone know how I can get a quantitative measure of the coverage of my target regions?
Moreover, I have few theoretical questions regarding the reference genome that should be used. Even if it is a target re-sequencing, is it correct to align my reads against the full genome? Indeed I have aligned against the full genome, but it also contained the clone contigs that can't be confidently placed on a specific chromosome (e.x. chrUn_gl000225 chrUn_gl000222, chr6_qbl_hap6, chrUn_gl000225). In your opinion is it correct or is it too much a conservative approach? Finally, as I have performed a target sequencing in which I masked the repeated regions, is it correct to align my reads directly against the masked genome?
Many thanks to anyone could help,
Sara
I need to analyze paired ends reads for a target re-sequencing experiment in which the repeated regions of my targets were masked.
I have performed the alignment with BWA and converted the export of BWA alignment in a SAM file. Then using SamTool I have removed duplicated reads and run the SNP and indel calling. Does anyone know how I can get a quantitative measure of the coverage of my target regions?
Moreover, I have few theoretical questions regarding the reference genome that should be used. Even if it is a target re-sequencing, is it correct to align my reads against the full genome? Indeed I have aligned against the full genome, but it also contained the clone contigs that can't be confidently placed on a specific chromosome (e.x. chrUn_gl000225 chrUn_gl000222, chr6_qbl_hap6, chrUn_gl000225). In your opinion is it correct or is it too much a conservative approach? Finally, as I have performed a target sequencing in which I masked the repeated regions, is it correct to align my reads directly against the masked genome?
Many thanks to anyone could help,
Sara
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