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Old 08-26-2015, 04:00 AM   #1
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Default Mapping: how to deal not unique mapping to homologous genes in different contigs


I'm trying to map some RNA-Seq reads to a fungus genome using the STAR aligner, and am subsequently using HTSeq to estimate the counts per gene. I am using an ENSEMBL genome fasta file and the corresponding GTF file. My problem is, the assembly consists of 413 super contigs, so I am unable to only use half of the homologous chromosomes (i.e. having a haploid reference) to avoid having my reads matched to multiple locations. Any suggestions for this? What is the most popular way to deal with this problem, namely the lack of fully assembled chromosomes and therefore the resulting inability to filter the homologous ones to avoid non-unique alignments?

Thanks in advance.
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