Computational protocol: Possible mechanisms of host resistance to Haemonchus contortus infection in sheep breeds native to the Canary Islands

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Protocol publication

[…] Raw sequence reads were first checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). The effect of trimming of low-quality nucleotides on genome alignment was examined using STAR algorithm. Raw sequence reads (FASTQ files) of 23 samples were mapped against the ovine reference genome Oar_v3.1 using STAR (v2.3.1t) with default parameters. The uniquely mapped read were used to count against the Ensembl annotation Oar_v3.1 for calculating the number of reads per gene. The counts of all samples were tabulated. This table was then inputted to DESeq for normalization and identification of differentially expressed genes between infection and control groups of both CHS and CS using the standard workflow as described. To correct for multiple hypothesis testing, the Benjamini-Hochberg procedure was used with an FDR cutoff of 0.05. Gene Ontology (GO) analysis over differentially expressed genes was performed using Fisher’s exact test. […]

Pipeline specifications

Software tools FastQC, STAR, DESeq
Databases Oar
Application Nucleotide sequence alignment
Organisms Haemonchus contortus, Ovis aries, Serinus canaria
Diseases Hair Diseases, Infection