User: sbchua.1990

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sbchua.199010
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Posts by sbchua.1990

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Book recommendation for the understanding of bioinformatic database
... Hi, I am looking for general knowledge about the linkage between databases such as KEGG, GO, COG. For example, how to convert result of blastp against nr database to EC number and also KEGG codes. I am more interested in getting broader view for practical purposes. ...
written 9 days ago by sbchua.199010
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Book recommendation for the understanding of bioinformatic database
... Hi, any recommendation for book regarding how today bioinformatic databases are structured and linked together. I need this to get a 'birds-eye view' on how today bioinformatic databases work. How and which databases accession no are linked together. Thanks in advance ...
genome gene alignment rna-seq blast written 11 days ago by sbchua.199010 • updated 11 days ago by 00Alireza.Tafazoli0010
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Comment: C: KEGG enrichment for non-model organism
... Thanks for reply, will clusterProfiler work for non-model species? Can I choose to use my own whole assembly as background? For simplicity, let say I have 10,000 genes assembled. 2,000 were annotated to at least one pathway (for background). I have 1,000 DEGs, 180 annotated to at least one pathway. ...
written 22 days ago by sbchua.199010
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KEGG enrichment for non-model organism
... Hi, just want to know if I have obtained KEGG annotation and mapped to pathway using KEGG mapper (http://www.genome.jp/kegg/mapper.html). Due to my lack of skill in doing the gene set enrichment analysis, I have think of a simpler way but not sure whether it is correct? I simply tabulate how many ...
gene R rna-seq written 5 weeks ago by sbchua.199010
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Comment: C: Clusterprofiler for KEGG enrichment (non-model species)
... Thanks for reply. Ko_number at second column. Do you have any suggestion for suitable software? ...
written 5 weeks ago by sbchua.199010
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Clusterprofiler for KEGG enrichment (non-model species)
... Hi, I wish to use clusterProfiler for KEGG pathway enrichment (non-model species, *Pleurotus pulmonarius*). I want to use my whole transcriptome as background. I now have files for whole transcriptome and DEG in the following format: TRINITY_identifier KO_number How can I proceed from h ...
gene R rna-seq written 5 weeks ago by sbchua.199010 • updated 16 days ago by Biostar ♦♦ 20
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Comment: C: Functional annotation pipeline
... Thanks for your reply. I would consider your recommendation. ...
written 9 weeks ago by sbchua.199010
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Functional annotation pipeline
... I have assembled a transcriptome using Trinity and clustering it using CD-hit with 0.95 threshold to reduce redundancy. For the clustered transcripts, I performed blastx against nr database (restricted to basidiomycota taxon due to computational power). I imported the blast result into blast2GO to ...
assembly sequence rna-seq blast written 9 weeks ago by sbchua.199010 • updated 10 days ago by colindaven260
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KEGG pathway and module enrichment for non-model fungi
... Hi, I am working on transcriptome of non-model fungi species. I have retrieved KOs from KEGG website and would like to perform enrichment analysis for biological interpretation. Any suggestion on softwares that can be used? I am new to transcriptome analysis. Correct me if I am wrong. When we per ...
gene blast rna-seq written 10 weeks ago by sbchua.199010
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Extract subset (based on GO or KEGG categories) from Trinotate.xls for goseq analysis
... Hi, I have assembled unigenes using Trinity pipeline and annotated them using Trinotate pipeline. How can I extract a subset of genes (based on GO or KEGG categories, for example oxidoreductases activity) from Trinotate.xls for goseq analysis? ...
gene R rna-seq written 11 weeks ago by sbchua.199010 • updated 11 weeks ago by h.mon7.5k

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