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[交流] 基因组测序方面的一些问题急

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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