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Multiple mapping pipelines have been developed to align individual RNA-seq reads to the corresponding genomes [ 23- 26].
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Many paired-end mapping pipelines simply discard reads that cannot be uniquely mapped.
Multi-copy loci are problematic for standard high-throughput sequencing mapping pipelines and are commonly discarded.
Relaxing the MQ filter applied in the pipeline can result in both sensitivity and precision > 95%%, however the MQ filter is applied to reduce the risk of false positives arising from multiple mapping hits for an integration – for instance if an integration were to occur within an interspersed repetitive element such as CR1.
Our mapping pipeline retains genomic mappings with one mismatch regardless of the location on the genome, or multiple mappings (threshold of 100 locations).
The original map contains multiple maps on one sheet.
JL and SG made disease mapping pipeline and PEIMAP pipeline initially and helped in manuscript writing.
Quality control was done using the eQTL mapping pipeline.
The ePSTs are generated using a proteogenomic mapping pipeline implemented in Perl.
The mapping pipeline was identical for both shotgun and captured samples.
A detailed description of the mapping pipeline is provided in the Supporting Information.
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