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Im Dokument suchen
Shah, Abhijeet; Hoffman, Joseph ; Schielzeth, Holger: Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size. In: BMC genomics. Jg.20 H. 1. 2019
Inhalt
Results
Transcriptome assembly assessment and completeness metrics
Transcriptome annotation and GO classification
SNP calling and estimation of minor all frequencies (MAF)
Scanning for expressed mitochondrial genes in assembled transcripts
Detection of Wolbachia Pel wPip strain sequences
Discussion
Conclusions
Methods
Sample collection
RNA extraction, cDNA library preparation and spike-in normalisation (step 1)
Pre-processing and sequence quality control and k-mer filtering (step 2)
Transcriptome assemblies (step 3)
Multi-assembly merging and duplicate contig reduction (step 4)
Transcript mapping and quantification (step 5)
Assessment of assembled transcriptome and contig filtering (step 6 and 7)
Annotation and sequence analysis (step 8)
SNP calling and estimation of minor allele frequencies
Searches for candidate green-brown pigmentation genes
Analysis of the mitochondrial genome
Additional files
Abbreviations
Acknowledgements
Funding
Availability of data and materials
Authors’ contributions
Ethics approval and consent to participate
Consent for publication
Competing interests
Publisher’s Note
References