简化基因组分析
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实际测试:
鸿元服务器 /home/bioinfo/radseq
process_radtags -p . -o 1-cleandata/ -e sbfI -c -q -r
zgrep TGCAGG --color=always SRR828261.1.fq.gz |head -n 20
//比对
bwa mem ../Gasterosteus_aculeatus.BROADS1.dna.toplevel.fa ../SRR828261.1.fastq |gzip -3 > SRR828261.1.sam.gz
//查看比对率
samtools flagstat SRR828303.1.sam.gz
//构建loci
gstacks -I ../2-align/ -M popmap -O output -t 8
//populations分析
populations -P ../3-build-loci/output/ -M ./popmap -r 0.65 --vcf --genepop --fstats --smooth --hwe -t 8 -
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python tagdigger_script.py -w . -b samples.csv -o mycounts.csv -k markerstokeep.txt --StacksTags ../ANCHA180152/ustack/catalog.tags.tsv.gz --StacksSNPs ../ANCHA180152/ustack/catalog.snps.tsv.gz --StacksAlleles ../ANCHA180152/ustack/catalog.alleles.tsv.gz
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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201254
A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates -
https://groups.google.com/g/stacks-users/c/1n6O98oWO2o/m/oRm3FYZTs1IJ?pli=1
Stacks不太适合多倍体（大于2）