BioScope Mapping Rounds
Hello
I am using BioScope 1.2 mapping pipeline to map SOLiD 50bp (fragment library) reads onto the Human genome.
About 60% of the reads were mapped when using the default mapping parameters (map.ini). However, some of the unmapped reads can - supposed there is no sequencing error and after translating them into nucleotide sequences - be mapped with Blast to the Human genome.
In order to increase mapping rate, repetitive mapping is mentioned in BioScope Book 1.2 but not well described. My questions are now
- how do you usually map genomic read data with BioScope to, for example, the Human genome, and
- are you using the default mapping parameters for 50 bp reads, how many mapping rounds, seed length, mismatches etc.
Many thanks for any hints and advice based on your experience in advance!
I am using BioScope 1.2 mapping pipeline to map SOLiD 50bp (fragment library) reads onto the Human genome.
About 60% of the reads were mapped when using the default mapping parameters (map.ini). However, some of the unmapped reads can - supposed there is no sequencing error and after translating them into nucleotide sequences - be mapped with Blast to the Human genome.
In order to increase mapping rate, repetitive mapping is mentioned in BioScope Book 1.2 but not well described. My questions are now
- how do you usually map genomic read data with BioScope to, for example, the Human genome, and
- are you using the default mapping parameters for 50 bp reads, how many mapping rounds, seed length, mismatches etc.
Many thanks for any hints and advice based on your experience in advance!
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