I'm a newbie to SOLiD data, please bear with me if this question has been asked before or sounds too naive.
I need to extract the number of reads for the reference from a small indel GFF file. Here are the field descriptions from the Bioscope document:
allele-counts field: The number of indel reads found for each of the alleles. The first item is always "REF". The number of reads found with the reference can be derived from the value of coverage_ratio.
coverage_ratio field: clipped ungapped coverage divided by the number of non-redundant gap alignment reads.
I just don't get it.
Say we have "REF, 4" in "allele-counts", coverage_ratio = 3.75, how to get the number of reads for the reference? Can anybody help? Thanks.
I need to extract the number of reads for the reference from a small indel GFF file. Here are the field descriptions from the Bioscope document:
allele-counts field: The number of indel reads found for each of the alleles. The first item is always "REF". The number of reads found with the reference can be derived from the value of coverage_ratio.
coverage_ratio field: clipped ungapped coverage divided by the number of non-redundant gap alignment reads.
I just don't get it.
Say we have "REF, 4" in "allele-counts", coverage_ratio = 3.75, how to get the number of reads for the reference? Can anybody help? Thanks.