User: jfo

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jfo10
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Posts by jfo

<prev • 13 results • page 1 of 2 • next >
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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 5 days ago by jfo10
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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 3 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 3 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 3 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 3 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 3 months ago by jfo10 • updated 3 months ago by Istvan Albert ♦♦ 80k
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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 4 months ago by jfo10
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Answer: A: calculating allele frequency difference or Fst value ?
... Hello Seta, [Here][1] are some quick answers to your questions. You can always try both methods to determine genetic differences in your populations of interest. Which method is more appropriate will depend on the hypotheses you want to test. For estimating genetic differentiation between populati ...
written 6 months ago by jfo10
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Comment: C: Changing Quality Scores Within Bam Files
... "usage (converts fastq 1.3/1.5 to sanger): samtools view -h in.bam | bam_rescale_quals.py - | samtools view -bS - > out.bam" So I guess, yea. ...
written 2.5 years ago by jfo10
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Computing Fst in multiple population using Popoolation2
... Dear everyone, I have a RNA-seq data for three populations: pooled individuals with at least n = 40 per library; two libraries each population (a total of 6 lib); around 40M PE reads per library). Objective: Get highest ranking SNPs using their Fst values to be used for SNP genotyping and pop gen ...
popoolation2 fst rna-seq written 2.6 years ago by jfo10

Latest awards to jfo

Popular Question 3 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 4 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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