{"id":555,"date":"2020-08-22T18:17:15","date_gmt":"2020-08-22T10:17:15","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=555"},"modified":"2020-08-22T18:17:15","modified_gmt":"2020-08-22T10:17:15","slug":"psmc%e5%88%86%e6%9e%90%e6%b5%81%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=555","title":{"rendered":"PSMC\u5206\u6790\u6d41\u7a0b"},"content":{"rendered":"<pre>\r\nbowtie2-build ..\/genome.fasta genome\r\nbowtie2 -x genome -p 80 -1 reads.1.fastq -2 reads.2.fastq -S bowtie2.sam\r\nsamtools sort -o bowtie2_sort.bam -O BAM -@ 40 -m 4G bowtie2.sam\r\n\/opt\/biosoft\/samtools-0.1.18\/samtools mpileup -C50 -uf ..\/genome.fasta bowtie2_sort.bam > gc_psmc.bcf\r\n\/opt\/biosoft\/samtools-0.1.18\/bcftools\/bcftools view -c gc_psmc.bcf > Pb_2G.vcf\r\nvcfutils.pl vcf2fq -d 10 -D 100 Pb_2G.vcf | gzip > diploid.fq.gz\r\n\/opt\/biosoft\/psmc-master\/utils\/fq2psmcfa -q20 diploid.fq.gz > diploid.psmcfa\r\n\/opt\/biosoft\/psmc-master\/utils\/splitfa diploid.psmcfa > split.psmcfa\r\n\/opt\/biosoft\/psmc-master\/psmc -N25 -t15 -r5 -p \"4+25*2+4+6\" -o diploid.psmc diploid.psmcfa\r\nseq 100 | xargs -i echo \/opt\/biosoft\/psmc-master\/psmc -N25 -t15 -r5 -b -p \"4+25*2+4+6\" -o round-{}.psmc split.fa | sh\r\ncat diploid.psmc round-*.psmc > combined.psmc\r\n\/opt\/biosoft\/psmc-master\/utils\/psmc_plot.pl -g x -u y combined combined.psmc\r\n# x\u4e3a\u8be5\u7269\u79cd\u7e41\u6b96\u4e00\u4ee3\u7684\u65f6\u95f4\uff0c\u6bd4\u5982\u4eba\u7684\u9ed8\u8ba4\u4e3a25\u5e74\uff0c\u8be5\u5904\u503c\u4e3a-g 25.\r\n# y\u4e3a\u8be5\u7269\u79cd\u78b1\u57fa\u66ff\u6362\u7387\uff0c\u53ef\u7531\u8fdb\u5316\u6811\u7684\u679d\u957f\u9664\u4ee5r8s\u8bc4\u4f30\u8be5\u7269\u79cd\u7684\u5206\u6b67\u65f6\u95f4\u5f97\u5230\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>bowtie2-build ..\/genome.fasta genome bowtie2 -x genome -p 80 -1 reads.1.fastq -2 reads.2.fastq -S bowtie2.sam samtools sort -o bowtie2_sort.bam -O BAM -@ 40 -m 4G bowtie2.sam \/opt\/biosoft\/samtools-0.1.18\/samtools mpileup -C50 -uf ..\/genome.fasta bowtie2_sort.bam > gc_psmc.bcf \/opt\/biosoft\/samtools-0.1.18\/bcftools\/bcftools view -c gc_psmc.bcf > Pb_2G.vcf vcfutils.pl vcf2fq -d 10 -D 100 Pb_2G.vcf | gzip > diploid.fq.gz \/opt\/biosoft\/psmc-master\/utils\/fq2psmcfa -q20 diploid.fq.gz > diploid.psmcfa [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/555"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=555"}],"version-history":[{"count":1,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/555\/revisions"}],"predecessor-version":[{"id":556,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/555\/revisions\/556"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=555"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=555"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=555"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}