<![CDATA[多倍体的SNP]]>https://www.cell.com/molecular-plant/pdf/S1674-2052(15)00130-6.pdf
Single Nucleotide Polymorphism Identification in
Polyploids: A Review, Example, and
Recommendations

]]>http://an.forum.genostack.com/topic/706/多倍体的snpRSS for NodeSat, 13 Jun 2026 14:27:44 GMTTue, 28 Jun 2022 03:13:37 GMT60<![CDATA[Reply to 多倍体的SNP on Thu, 21 Jul 2022 05:51:58 GMT]]>https://www.frontiersin.org/articles/10.3389/fgene.2020.00222/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Genetics&id=521391
Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut

该文献对异源多倍体的snp分析对比了5种流程 可以重点看看

]]>http://an.forum.genostack.com/post/1718http://an.forum.genostack.com/post/1718Thu, 21 Jul 2022 05:51:58 GMT<![CDATA[Reply to 多倍体的SNP on Thu, 21 Jul 2022 02:57:07 GMT]]>https://www.frontiersin.org/articles/10.3389/fgene.2020.00222/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Genetics&id=521391

Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut

]]>http://an.forum.genostack.com/post/1717http://an.forum.genostack.com/post/1717Thu, 21 Jul 2022 02:57:07 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 20 Jul 2022 12:30:49 GMT]]>https://gist.github.com/sbamin/27acf13f2a28161efbf89a273559bca4
https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignment

sambamba view -t 12 -h -f bam -F "mapping_quality >= 1 and not (unmapped or secondary_alignment) and not ([XA] != null or [SA] != null)" test.bwa-mem.bam -o test-uniq.bam

获取唯一比对的序列

]]>http://an.forum.genostack.com/post/1716http://an.forum.genostack.com/post/1716Wed, 20 Jul 2022 12:30:49 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 20 Jul 2022 11:27:25 GMT]]>https://api.research-repository.uwa.edu.au/ws/portalfiles/portal/57891001/THESIS_DOCTOR_OF_PHILOSOPHY_SCHEBEN_Armin_2019.pdf
THESIS_DOCTOR_OF_PHILOSOPHY_SCHEBEN_Armin_2019.pdf
这个文章里面说可以通过比对后的质量值 筛选比对到多个位置的序列

]]>http://an.forum.genostack.com/post/1715http://an.forum.genostack.com/post/1715Wed, 20 Jul 2022 11:27:25 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 20 Jul 2022 11:07:38 GMT]]>A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-100

]]>http://an.forum.genostack.com/post/1714http://an.forum.genostack.com/post/1714Wed, 20 Jul 2022 11:07:38 GMT<![CDATA[Reply to 多倍体的SNP on Fri, 08 Jul 2022 07:06:12 GMT]]>SNP Discovery in Complex Allotetraploid Genomes
(Gossypium spp., Malvaceae) Using Genotyping by
Sequencing
apps.1400077.pdf

]]>http://an.forum.genostack.com/post/1663http://an.forum.genostack.com/post/1663Fri, 08 Jul 2022 07:06:12 GMT<![CDATA[Reply to 多倍体的SNP on Fri, 01 Jul 2022 11:06:11 GMT]]>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356317/
ba57d465-2ab9-46a9-9896-849da064666d-image.png

]]>http://an.forum.genostack.com/post/1641http://an.forum.genostack.com/post/1641Fri, 01 Jul 2022 11:06:11 GMT<![CDATA[Reply to 多倍体的SNP on Thu, 30 Jun 2022 10:47:50 GMT]]>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062318/
Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica

]]>http://an.forum.genostack.com/post/1629http://an.forum.genostack.com/post/1629Thu, 30 Jun 2022 10:47:50 GMT<![CDATA[Reply to 多倍体的SNP on Thu, 30 Jun 2022 02:55:51 GMT]]>genes-11-01220-v2.pdf
b3e2d517-30ea-4fe1-8adc-58f82683f1d0-image.png
这个文献研究了花生 花生也是一个异源四倍体 相似的文献可以重点看看
这个流程结合了GATK+Sweep

]]>http://an.forum.genostack.com/post/1617http://an.forum.genostack.com/post/1617Thu, 30 Jun 2022 02:55:51 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 20 Jul 2022 05:59:03 GMT]]>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920642/
Homoeologs: What Are They and How Do We Infer Them?
Homoeologs are pairs of genes that originated by speciation and were brought back together in the same genome by allopolyploidization.
Homoeologs are not necessarily one-to-one or positionally conserved.
部分同源指的是基因经过不同的演化后，又因为异源杂交，被放到了同一个基因组中。
allopolyploids result from genome doubling following a hybridization between two different species (interspecific), whereas autopolyploids result from genome doubling within one species (intraspecific).

cd057de5-8107-4caa-b112-4394e381ca7e-image.png
a284a42b-0fd3-4721-8705-c9adfcb566c3-image.png

473426ad-5964-486c-9918-7c5f85f0f294-image.png

https://lab.dessimoz.org/blog/2016/03/24/what-are-homoeologs
Last but not least, we learned that even though homoeolog has alternatively been spelled “homeolog” (no extra o), homoeolog is the clear winner in terms of popularity.
homoeolog有时候也被写作homeolog

]]>http://an.forum.genostack.com/post/1614http://an.forum.genostack.com/post/1614Wed, 20 Jul 2022 05:59:03 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 29 Jun 2022 07:47:17 GMT]]>https://max.book118.com/html/2014/0318/6706569.shtm
多倍体植物中单核苷酸多态性（SNPs）的开发

]]>http://an.forum.genostack.com/post/1613http://an.forum.genostack.com/post/1613Wed, 29 Jun 2022 07:47:17 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 29 Jun 2022 07:46:49 GMT]]>https://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2011.00644.x
8c567351-00c5-45ad-aff3-5f2944bfe732-image.png

]]>http://an.forum.genostack.com/post/1612http://an.forum.genostack.com/post/1612Wed, 29 Jun 2022 07:46:49 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 29 Jun 2022 07:16:39 GMT]]>https://sci-hub.st/10.1007/s00438-008-0365-y
Identification of homologous, homoeologous and paralogous sequence variants in an outbreeding allopolyploid species based on comparison with progenitor taxa

]]>http://an.forum.genostack.com/post/1611http://an.forum.genostack.com/post/1611Wed, 29 Jun 2022 07:16:39 GMT<![CDATA[Reply to 多倍体的SNP on Tue, 28 Jun 2022 07:08:50 GMT]]>https://www.cerealsdb.uk.net/cerealgenomics/WheatBP/Documents/DOC_Homoeologous_vs_Varietal_SNPs.php#:~:text=a)%20A%20homoeologous%20SNP%20exist,characteristic%20of%20a%20single%20individual.

f5079740-c201-4ed8-a677-97add82c924e-image.png

]]>http://an.forum.genostack.com/post/1603http://an.forum.genostack.com/post/1603Tue, 28 Jun 2022 07:08:50 GMT<![CDATA[Reply to 多倍体的SNP on Tue, 28 Jun 2022 07:02:32 GMT]]>https://www.biorxiv.org/content/10.1101/2022.04.21.488948v1.full
CAPG: Comprehensive Allopolyploid Genotyper
2d4f0652-ed0c-4fe8-9247-a05df996cb78-image.png
异源四倍体SNP的2种类型
Distinguishing homoeologous and allelic SNPs.
Allotetraploid genomes for two individuals, subgenome A (left), subgenome B (right). Pink loci are homoeologous SNPs, different between and constant within subgenomes. Other colored loci are allelic SNPs, green in subgenome A, red in subgenome B. The dark green and brown loci are homozygous. The light green and red loci are heterozygous in one of the individuals.

]]>http://an.forum.genostack.com/post/1602http://an.forum.genostack.com/post/1602Tue, 28 Jun 2022 07:02:32 GMT<![CDATA[Reply to 多倍体的SNP on Wed, 20 Jul 2022 06:25:26 GMT]]>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555216/
SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops

https://edepot.wur.nl/441939
SNP detection in
allopolyploid crops
using NGS data
这篇文章对sweep做了评估

]]>http://an.forum.genostack.com/post/1601http://an.forum.genostack.com/post/1601Wed, 20 Jul 2022 06:25:26 GMT<![CDATA[Reply to 多倍体的SNP on Tue, 28 Jun 2022 06:18:18 GMT]]>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791807/
SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species

]]>http://an.forum.genostack.com/post/1600http://an.forum.genostack.com/post/1600Tue, 28 Jun 2022 06:18:18 GMT