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基因组测序方面的一些问题 急
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刚遇到一些问题，板上有这方面的专家吧，简单指导回答一下如何，特别是不同alignment depth ，提供一些学习资料也行哦，谢谢了 我的 email honglinzhou@163.com A. The attached file shows coverage-depth distributions for alignments of sequencing reads against a genome. How do you explain the differences between the three distributions? B. In preparing the library to be sequenced, a certain enrichment process was carried out (digestion with methylation-sensitive enzymes), with the intention of enriching the library in expressed sequences. Can you suggest a computational method for determining whether this process was effective? C. Suppose it is determined that for SNP detection we will need to achieve an alignment depth of 12 over at least 0.05 of the sorghum genome. How many genome equivalents of DNA should be sequenced? D. Given the results of genotyping 250,000 SNPs in twenty other sorghum accessions, how would you handle these data? How would you evaluate and describe the polymorphism between these accessions? E. If requested to develop and report a comparative genomic analysis based on the above results, how would you approach it? attached file Sampling from In silico sampling from Actual reads from simulated genome sorghum genome Tx430 Depth Bases Proportion Bases Proportion Bases Proportion 0 23570121 0.786 24908179 0.830 25086953 0.836 1 5687926 0.190 4525394 0.151 3524933 0.117 2 686179 0.023 522370 0.017 851887 0.028 3 52222 0.002 40975 0.001 269292 0.009 4 3285 0.000 2326 0.000 109642 0.004 5 104 0.000 141 0.000 52132 0.002 6 13 0.000 22 0.000 29562 0.001 7 18727 8 12008 9 9091 10 6404 11 4675 12 3622 13 2637 14 2217 15 1731 16 1508 17 1305 18 1059 19 963 20 892 21 2217 22 1731 23 1508 24 1305 25 1059 26 963 27 892 ... ...[extends to depth 289] Coverage-depth distributions for two computer experiments and a real DNA sequencing experiment. 225,959 32-base reads were sampled from a computer-simulated random 30-Mb genome with GC proportion 0.432 (like that of the sorghum genome) or from 30 Mb of the sorghum genome assembly. Alternatively, 225,959 actual reads that aligned to the same 30-Mb genome tract were used. All reads were aligned to their source DNA with SOAP and the depth distribution of unique alignments was tabulated. Omitted from the table is the very long tail of the distribution for the real dataset, extending to a depth of 289. [search]genome sequence[/search] |
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2楼2008-05-26 13:25:24
