ITS Plant Coverage
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评估
- 难度
- 5/5
- 预计耗时
- 一周以上
- 新手友好度
- 25/100
- Issue 类型
- 功能
- 描述清晰度
- 需要澄清
- 活跃度
- 停滞
- 技术栈
- r
- 领域
- bioinformatics, data
调研方向
Start by locating the complete species list, sequence reads file, OTU-Taxon linker file, and any existing voucher or TrnL/ITS analysis. Work through each checklist question, including the proposed ITS OTU-Taxon linker and BLAST comparison. Done means the requested counts, flagged shared OTUs, and candidate external sequences are documented.
由索引模型根据 Issue 内容生成。
描述
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How many voucher species from that list have had TrnL run
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How many have a "good" ITS read?
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How many species on the complete species list do we find being identified in the poop samples that we do not have vouchers for (i.e. they are identified at the species level in the sequence reads file)
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How many species from our complete list have a ITS sequence in the OTU-Taxon linker file but the sequence is identical to other species? (this one will require us to create a ITS OTU-Taxon linker)
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For species with a OTUID that is shared with other species in the OTU-Taxon Linker, is there only one species from our site in that group? (i.e. do we feel like we could assign that OTU to one of our species as a flagged low-quality DNA sequence)?
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Check our species list against BLAST, are there high quality sequences in the database that we could add to ours with a source flag to indicate that we did not run a voucher speciment but are "latin name" matching with BLAST?
- 主要语言
- R
- 星标
- 0
- 派生
- 1
- PR 合并指标
- 30 天内没有已合并 PR
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- 提交 Pull Request，并在描述里引用这个 Issue 编号。
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