User: Biogeek

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Biogeek400
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Posts by Biogeek

<prev • 186 results • page 1 of 19 • next >
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Answer: A: Renaming Entry In Fasta File
... `sed 's/NODE/lclav_contig/' {INPUT FILE} | sed 's/_/ /g' | sed 's/ /_/1' > {OUTPUT FILE}` *Apologies, should have replied inline. ...
written 5 weeks ago by Biogeek400
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Comment: C: Retrieve multiple refseq genomes in seperate fasta files
... Good call genomax, thanks! I've now installed the Entrez utilities and can obtain my record with efetch. I'll write a loop using the 'list.txt' file I have which contains accession numbers. One more question, apologies for the ignorance (as required), is there a way I can also obtain my .fasta file ...
written 5 weeks ago by Biogeek400
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Retrieve multiple refseq genomes in seperate fasta files
... I've had a search and I can't seem to find any relatable questions. My task is as follows: 1. I have a list of Refseq accessions in a .txt file. 2. I want to download all the associated genomes to seperate .fasta files in a local directory. I note that I can use Entrez or NCBI assembly downloa ...
ncbi genome download refseq written 5 weeks ago by Biogeek400
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Bioinformatics workstation Spec advice: Metagenomics
... Hey fellow Biostars, I'm tasked with buying a workstation for my research group (metagenomics) and would like some advice/pointers. I know this question has been asked several times before; however, given that tech advances each year, I thought it would be appropriate to ask it again in 2020. A wor ...
metagenomics ram workstation written 3 months ago by Biogeek400
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Comment: C: General question about batch effect, read trimming and what to do when the adapt
... Mozart, the paired files are what you use. I just want to confirm with you though...Are they the correct Adaptor sequences that your sequencing was performed with? It may be that the adaptor sequences were removed by the facility, common. As such, very low % of reads will be trimmed.. [Link to Next ...
written 15 months ago by Biogeek400
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Comment: C: gene IDs enrichment in plants
... What sort of data do you want to carry out an enrichment on? Also what plant are you working with, is it a model or a non-model? ...
written 15 months ago by Biogeek400
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Answer: A: General question about batch effect, read trimming and what to do when the adapt
... I'd recommend using BBDUK under the bb tools suite by Brian Bushnell. It has an extensive adapter.fa file containing all publicly available adaptor sequences - just an idea? The amount of times people sue Trimmomatic without the correct adaptor sequence .fa file. Admittedly I also made that mistake ...
written 15 months ago by Biogeek400
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Answer: A: Making a Group Tree using RNA-seq Read Count in R
... Hi Minuate, Can you please specify what sort of 'tree'? Do you mean a heatmap or dendrogram based figure? If so you can use heatmap.2 or pheatmap in R. In conjunction with ggplots2 and other various R modules, you can make some pretty nice diagrams. If that count data is normalised, you can log2 t ...
written 15 months ago by Biogeek400
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Confused with Fishers test for GO enrichment
... Hi, I'm running the fisher.test function in R. My code is: dfx <- input_fishers res1<- NULL for (i in 1:nrow(dfx)){ table1 <- matrix(c(dfx[i,1], dfx[i,2], dfx[i,3], dfx[i,4]), ncol = 2, byrow = TRUE) p1<- fisher.test(table1, alternative = "greater")$p.value res1 ...
fishers input enrichment written 15 months ago by Biogeek400
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Example of gene2cat goseq
... Any examples of the gene2cat input for a non-model organism? I'm working in R. My first column is GO:XXXXXX and my second column is gene ID. Row names are numerical (automatic). To be fair the Vignette and guides aren't so clear considering a lot of people use it for non-model organisms. I'm gettin ...
goseq written 15 months ago by Biogeek400 • updated 15 months ago by cfos4698170

Latest awards to Biogeek

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Any tools out there for Interproscan enrichment analysis?
Popular Question 7 months ago, created a question with more than 1,000 views. For Any tools out there for Interproscan enrichment analysis?
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Popular Question 8 months ago, created a question with more than 1,000 views. For RNA-Seq of environmental samples
Great Question 15 months ago, created a question with more than 5,000 views. For Paired End Trimmomatic producing asymmetric paired read files.
Great Question 15 months ago, created a question with more than 5,000 views. For MDS plots with R
Popular Question 15 months ago, created a question with more than 1,000 views. For RNA-Seq of environmental samples
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Popular Question 20 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Popular Question 2.4 years ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Popular Question 2.4 years ago, created a question with more than 1,000 views. For curating a viridiplantae database
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