您好怀伦！是否可以給我一個(gè)詳細(xì)的代碼威恼，謝謝
用blast進(jìn)行短序列（20nt左右）的搜索一句話概括就是：blastn多加上-task blastn-short -word_size 7 -evalue 1就ok了卧抗。 這段時(shí)間用blastn比較多沾谓，所以遇到這個(gè)問題...
IP屬地：北京
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您好！我想咨詢一下，基因組組裝除了染色體序列外還剩余一些scaffolds序列，這些序列是不是未定位到染色體上的序列唧领，而且這些序列的重復(fù)性比較高？我這樣理解是不是對的
一文看懂三代組裝軟件——Flye
作者：童蒙編輯：angelica 一雌续、介紹 Flye是用于單分子組裝數(shù)據(jù)的denovo基因組裝的軟件斩个。這個(gè)軟件可以用于各種數(shù)據(jù)集，從小的細(xì)菌到大的哺乳動(dòng)物驯杜。 輸入是原始的Pa...
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@黃甫一 好的受啥，謝謝你的答復(fù)
跨物種同源基因轉(zhuǎn)換（biomaRt和homologene）2022-06-17
適用背景 當(dāng)我們進(jìn)行跨物種比較分析時(shí)會(huì)發(fā)現(xiàn)基因名對不上，或者找不到基因鸽心，這時(shí)候就需要進(jìn)行物種間的同源基因轉(zhuǎn)換滚局。最常用的工具就是Ensembl的biomaRt，另外還查到NCB...
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@黃甫一謝謝您的回答顽频。想讓您幫我看一下文章了里面寫到了核畴，對于解決one to many和many to many問題的方法，建立了元基因這個(gè)是怎么做的冲九，原文如下：
Ortholog gene selection
To compare transcription between species, we first created a gene ortholog table using the mouse genome as the reference gene list. We performed gene homology search, using ensemble multiple species comparison tool (http://www.ensembl.org/biomart/martview/42ddd77f8b0f4aae7d9eefe32cc4518c). Each species was compared to mouse and a high-quality ortholog genes list was extracted (gene order conservation score above 75, whole genome alignment score above 75 and minimum sequence identity above 80%). To account for gene paralogs and gene-duplication events, an aggregated table of ‘‘meta-genes’’ was created. Each meta-gene may include all gene symbols homologous to one mouse gene. For each organism, read counts were combined across all manifestations of each meta-gene. For example, if zebrafish’s actb1 had two reads, and actb2 three reads, the actb meta-gene received a total of five reads. Missing genes in species were given an ‘‘A’’ value.跨物種同源基因轉(zhuǎn)換（biomaRt和homologene）2022-06-17
適用背景 當(dāng)我們進(jìn)行跨物種比較分析時(shí)會(huì)發(fā)現(xiàn)基因名對不上，或者找不到基因跟束，這時(shí)候就需要進(jìn)行物種間的同源基因轉(zhuǎn)換莺奸。最常用的工具就是Ensembl的biomaRt，另外還查到NCB...
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您好冀宴！我想問下結(jié)果中存在many to many如何處理灭贷？
跨物種同源基因轉(zhuǎn)換（biomaRt和homologene）2022-06-17
適用背景 當(dāng)我們進(jìn)行跨物種比較分析時(shí)會(huì)發(fā)現(xiàn)基因名對不上，或者找不到基因略贮，這時(shí)候就需要進(jìn)行物種間的同源基因轉(zhuǎn)換甚疟。最常用的工具就是Ensembl的biomaRt仗岖，另外還查到NCB...
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@七樓的白羊 謝謝你
【轉(zhuǎn)】Reading KEGG annotation online: fail to download KEGG data... Error in download.KEGG.Path(spe...
本文轉(zhuǎn)載自：http://www.360doc.com/content/22/0604/23/76149697_1034565139.shtml 最近在做KEGG富集分析時(shí)，...
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您好檩电！我想問一下，我的協(xié)議已經(jīng)是auto了府树，不知道為什么依然報(bào)相同的錯(cuò)俐末，請大神指點(diǎn)一下：
> getOption("clusterProfiler.download.method")
[1] "auto"
> KEGG<-enrichKEGG(gene$ENTREZID,#KEGG富集分析
+ organism = GO_database,
+ keyType = 'kegg', #KEGG 富集
+ pvalueCutoff = 0.05,
+ qvalueCutoff = 0.05)
Reading KEGG annotation online:
fail to download KEGG data...
Error in download.KEGG.Path(species) :
Failed to download KEGG data. Wrong 'species' or the network is unreachable. The 'species' should be one of organisms listed in 'https://www.genome.jp/kegg/catalog/org_list.html'【轉(zhuǎn)】Reading KEGG annotation online: fail to download KEGG data... Error in download.KEGG.Path(spe...
本文轉(zhuǎn)載自：http://www.360doc.com/content/22/0604/23/76149697_1034565139.shtml 最近在做KEGG富集分析時(shí)，...
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您好！作者垄潮，我想咨詢一下烹卒，這個(gè)biomaRT包和biomart數(shù)據(jù)庫中的不同物種之前同源基因名稱的轉(zhuǎn)換，依據(jù)序列相似性（或者同源）是多少魂挂？
biomaRt: 用R愉快檢索BioMart數(shù)據(jù)庫
網(wǎng)速慢的原因找到了 R 與 BioMart 數(shù)據(jù)庫的語言接口 (interface) Durinck S, Spellman P, Birney E, Huber W (20...
