User: nbvasani

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nbvasani230
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5 years ago
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6 years, 2 months ago
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Posts by nbvasani

<prev • 87 results • page 1 of 9 • next >
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Comment: C: Merge 2 de novo assembly generated using Trinity?
... Hi Prakki! Thanks for the suggestion. The main resion why I didn't want to create new assembly: 1] My previous assembly is 80% annotated. 2] My new RNA-seq data consist of 550million reads and if I use this reads to generate assembly it will used my whole PC memory and will freeze the PC. Thank ...
written 5.1 years ago by nbvasani230
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Comment: C: Merge 2 de novo assembly generated using Trinity?
... Thanks Rayan! Advice on thread is vice-versa. Thanks for all link and suggestion. Naresh     ...
written 5.1 years ago by nbvasani230
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Merge 2 de novo assembly generated using Trinity?
... Hi Fellow Users, In past I have generated transcriptome de novo assembly for plant using trinity and annotated about 90% of assembly. Recently I got RNA-seq data from hiseq illumina of same plant. So this time I mapped new rna-seq data to existing assembly and unmapped reads were extracted. I used ...
assembly rna-seq transcriptome written 5.1 years ago by nbvasani230 • updated 5.1 years ago by Prakki Rama2.3k
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Comment: C: Plant Annotation Workflow
... Great! Contact author of that articles they will suggest how they annotated their assembly. ...
written 5.6 years ago by nbvasani230
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Comment: C: Plant Annotation Workflow
... Hi User000, Is any NGS article related to your plant species published? You might get some clue for your anoatation from that article. If it's ok with you, can you tell me your plant species? ...
written 5.6 years ago by nbvasani230
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Comment: C: Plant Annotation Workflow
... You are right Arabidopsis alone is not the best choice. But he has to start from some plant db in order to annotate his assembly. If you have any suggestion let User000 know instead of making unnecessary statement. ...
written 5.6 years ago by nbvasani230
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Comment: C: Plant Annotation Workflow
... It all depends on what you want from your data. With DGE list it will be faster. ...
written 5.6 years ago by nbvasani230
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Comment: C: Plant Annotation Workflow
... You can generate Differential Gene expression (DGE) list by using R package i.e. edgeR and DEseq. ...
written 5.6 years ago by nbvasani230
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Comment: C: Plant Annotation Workflow
... Yap, it generally take a week or so. Instead of concentrating on whole de novo assembly, try to generate DGE list, then run blastx against all db you have. DGE list will be easy to handle compare to de novo assembly and you will get your result faster. Let say you still find less number of hits, you ...
written 5.6 years ago by nbvasani230
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Comment: C: Plant Annotation Workflow
... I agree with "Arabidopsis thaliana is a species that has a per base pair substitution rate several times higher than the average angiosperm." As per my understanding, best route to start annotation is to start with plant species which is well studied and resemble to your plant species. ...
written 5.6 years ago by nbvasani230

Latest awards to nbvasani

Student 5.3 years ago, asked a question with at least 3 up-votes. For Create Heat Map Using Edger Output Data
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Fastx_Collapser Has No Fastq Output
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Create Heat Map Using Edger Output Data
Popular Question 5.5 years ago, created a question with more than 1,000 views. For How Logfc Value Is Calculated In Edger?
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