Petromyzon marinus Germline Specific Regions

Analysis NamePetromyzon marinus Germline Specific Regions
MethodBWA-MEM (v.0.7.10)
Date performed2017-12-13
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Identification and Characterization of Germline-Specific/Enriched Sequences: To identify germline-specific regions, we separately aligned paired end reads from blood and sperm DNA to the germline genome assembly using BWA-MEM (v.0.7.10) with default parameters and filtered to exclude unmapped reads and supplementary alignments (samtools v.1.2 with option: view -F2308). Initial coverage analyses was implemented using bedtools v2.23.0 and revealed that the modal coverage of reads from sperm DNA was slightly lower than the coverage of reads from blood, ~73X and ~80X, respectively, but contained a larger amount of low-copy DNA. To identify germline-enriched intervals, data were filtered to remove regions with coverage both from sperm and blood of < 10 (underrepresented regions: computed with genomecov -bga, bedtools v2.23.0) and also regions with coverage exceeding three times the modal value in sperm or blood (high-copy regions). The remaining data were processed to generate coverage ratios for discreet intervals containing 1,000 bp (or >500 bp at contig ends) of approximately single-copy sequence. Identification of contiguous intervals and re-estimation of coverage ratios was performed using DNAcopy version 1.42.0 after removing trailing windows that were less that 500bp in length. Ontology analyses used naming assignments that were generated using multispecies blast alignments via MAKER and were performed using Enrichr.