User: jfo

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jfo10
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Posts by jfo

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GO annotation on diamond blasted transcriptome (nr db)
... Hello! So far, Approaches to GO annotation of transcriptomes of non-model organisms (besides B2G) point to the use of Trinotate and Genescf. I would like to ask if there is an easy way to directly add GO annotation to a diamond blast result (against NCBI nr)? Since B2G is really slow on a basic sub ...
diamond go blast rna-seq written 5 weeks ago by jfo10
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Comment: C: GeneBank accession 2 Entrez gene id
... Hi! How do we use this for accessions representing multiple organisms, especially non-model ones? for example: XP_021371371.1 and PIK53657.1 ...
written 5 weeks ago by jfo10
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Comment: C: Kissplice2reftranscriptome error : IndexError
... Thank you Vincent! Everything went smoothly now. :) ...
written 7 months ago by jfo10
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Kissplice2reftranscriptome error : IndexError
... Hello, I am trying to run the last part of kissplice pipeline, which is kissplice2reftranscriptome and got this error: command: > kissplice2reftranscriptome -b ORP_corset_all_longest.fasta.transdeco > der.bed -k > kissplice_out_Fask41_coherents_type_0a.fa > -t out_blat_SNP_ORP_ID_80.p ...
k2rt snp rna-seq kissplice written 8 months ago by jfo10 • updated 7 months ago by vincent.lacroix130
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Answer: A: How to generate KEGG pathway classification chart
... This graph could definitely be generated using grouped bar plot in R (ggplot2). To get the KEGG Pathways and their corresponding values, you should run KEGG reconstruction (https://www.genome.jp/kegg/tool/map_pathway.html) using your KOs. Format the resulting file to a table that will be used in R ...
written 11 months ago by jfo10
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Comment: C: how to perform the RealignerTargetCreator when there is not this algorithm anymo
... In my case, I need the indel Realignment for other variant callers such as Lofreq and CRISP. Also, I get the same exact error even if I just use: gatk --list ...
written 12 months ago by jfo10
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Comment: C: Genbank GI accession format for DAVID input
... I have the Official Gene Symbols, which actually works. My confusion comes from the use of the unigenes with nr hits but with no gene symbols. Should I just proceed with those which had gene symbols? This is why I was looking for a way to get all these unigenes with nr hits to have other accession n ...
written 12 months ago by jfo10
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Comment: C: Genbank GI accession format for DAVID input
... Thank you for the prompt answer. I do have the accessions; however, I am not sure how to use different input types for the analysis in DAVID. For example I have ref (mostly XP_), dbj, gb, or sp for the accessions. How do I convert these accession IDs to a DAVID-"interpret-able" format? I am having ...
written 12 months ago by jfo10
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Genbank GI accession format for DAVID input
... Hi! I would like to seek an advice or two with regard to the proper format of GENBANK_GI_ACCESSION for DAVID Function Analysis. I tried these formats: 1. gi123456 2. gi|123456 3. 123456 Sadly, nothing worked. I could not find any examples. I prefer gi accessions for this because all my unigenes o ...
david functional analysis written 12 months ago by jfo10 • updated 12 months ago by Istvan Albert ♦♦ 82k
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Answer: A: Any web server for KOG annotation for denovo transcriptome assembly?
... You can upload your pep files [here][1]. Then graph the results using the R code [here][2]. [1]: http://%20http://weizhong-lab.ucsd.edu/webMGA/server/kog/ [2]: https://stackoverflow.com/questions/39613006/how-to-add-main-title-and-manipulating-axis-labels-in-ggplot2-in-rstudio?noredirect=1&am ...
written 13 months ago by jfo10

Latest awards to jfo

Popular Question 11 months ago, created a question with more than 1,000 views. For Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)
Popular Question 13 months ago, created a question with more than 1,000 views. For Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)

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