基因数据处理21之BWASW算法ref分块建立索引然后比对（ref切分为
发布时间：2021-05-18 08:15:43 所属栏目：大数据 来源：网络整理
导读：1.时间分析 对ref为单条染色体进行比对，第一次比对在3-5s不等，对chr1-4比对，在20s左右 连续比对多次后，对单染色体比对降到1s左右，chr1-4降到2s左右 不懂为什么比一次比对时间比较长，后面几次比对时间变短 运行代码： hadoop@Master:~/cloud/adam/xubo/
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr1.sam 264 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 105 + 0 mapped (39.77% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr2.sam 260 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 83 + 0 mapped (31.92% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr3.sam 256 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 80 + 0 mapped (31.25% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr4.sam 254 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 58 + 0 mapped (22.83% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr1-4.sam 264 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 146 + 0 mapped (55.30% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)3.比对结果文件，太长，就不粘了 （编辑：ASP站长） 【免责声明】本站内容转载自互联网，其相关言论仅代表作者个人观点绝非权威，不代表本站立场。如您发现内容存在版权问题，请提交相关链接至邮箱：bqsm@foxmail.com，我们将及时予以处理。 |
相关内容
未处理完善
-
无相关信息
最新更新