User: Biogeek

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Biogeek380
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Posts by Biogeek

<prev • 183 results • page 2 of 19 • next >
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Split comma seperated list of GO terms into multiple rows and maintain gene identifier in each
... I have a tab separated dataset, although the GO terms are comma separated. GENEID1 GO:XXXXX,GO:YYYYYY,GO:ZZZZZZ I want to make it so that the dataset becomes a tab-seperated dataset where each GO term is represented on a new line with the gene identifier: GENEID1 GO:XXXXX GENEID1 ...
gene ontology data manipulation written 13 months ago by Biogeek380 • updated 13 months ago by st.ph.n2.5k
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ReviGO down, any alternatives for GO enrichment condensing?
... Any alternatives to ReviGO? I'm looking to condense the results of TopGO results so I get a clearer picture of the main processes occuring in my organism? ReviGO is down.I have a list of GO terms and P-values to pipe in. I had used ReviGO for initial analysis and it worked well. Many thanks! ...
revigo simrel topgo go enrichment written 13 months ago by Biogeek380 • updated 13 months ago by Berghopper20
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Enrichment via simple Fishers exact: Combine or not?
... Here's the scenario. I have a list of GO terms representative of an upregulated gene set. I am using the number of occurances of a unique GO in the upregulated gene set as my test set, the number of total upregulated genes as my test population. My reference set is the occurances of that unique GO ...
enrichment fishers go statistics written 13 months ago by Biogeek380
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Comment: C: slurm Exceeded step memory limit: Interleaving FastQ files
... Always saving the day Genomax. Thank you very much. I've used BBDUK. I'll run that now and report back! ...
written 14 months ago by Biogeek380
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slurm Exceeded step memory limit: Interleaving FastQ files
... Dear all, I am interleaving FastQ files (total combined 32GB (16GB each)). I've provided the script with 1 node and 26GB RAM for processing. Basic command as below: paste $1 $2 | paste - - - - | awk -v OFS="\n" -v FS="\t" '{print($1,$3,$5,$7,$2,$4,$6,$8)}' No matter how much mem I give the ...
fastq slurm written 14 months ago by Biogeek380
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Comment: C: Sequencing (+1bp in length?) and adaptor trimming.
... Genomax, Many thanks, this is an informative answer. Base pairs range from 31-76bp in size. Don't all seem to be the one length. I'd assume they have been trimmed based on your statements. I've emailed the sequencing provider once more, should know soon. Do most people leave that +1bp in and call i ...
written 14 months ago by Biogeek380
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Sequencing (+1bp in length?) and adaptor trimming.
... Dear all, I've been told 75bp paired end sequencing was performed on recent RNA. FastQC says sequence lengths are 76bp, as does an awk script I ran on my .fastq files. Can anyone explain why the sequencing centre said 75bo was performed when I'm counting 76bp? Sequencer was a nextseq500 with Truseq ...
adapters rna-seq sequencing written 14 months ago by Biogeek380 • updated 14 months ago by genomax83k
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Get -400bp to +50bp sequence of gene from gff3 file
... Dear all, I have used bedops and bedtools to obtain -2000bp upstream of my gene start (based on gff3 coordinates) file and the scaffold fasta file of the genome.While I know how to get upstream, I do; however want to get per say +50bp upstream of the gene start too. Is there a way of getting the re ...
upstream promoter downstream motifs written 16 months ago by Biogeek380 • updated 16 months ago by Alex Reynolds30k
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Gene correlation analysis after deseq2
... I have 8 RNA libraries (4 reps per each of two conditions - tissue specific). I have approx 500 genes upregulated and 100 genes downregulated in the tissue of interest. I have a matrix of deseq2 normalised counts for all of the genes which I've pulled the differently expressed gene records from. ...
deseq2 correlation clustering written 17 months ago by Biogeek380 • updated 17 months ago by dqz3779779050
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Multiple fasta file : calculate % composition of amino acids
... I've come across Expasy protein param... it's limited in the sense you can only copy/paste 1 sequence at a time. Is there an alternative approach via command line to calculate alphabet % composition of each >sequence? I haven never ventured into Biopython. I mostly use R and command line. All he ...
calculate amino acids composition written 17 months ago by Biogeek380 • updated 17 months ago by Pierre Lindenbaum128k

Latest awards to Biogeek

Popular Question 5 months ago, created a question with more than 1,000 views. For Any tools out there for Interproscan enrichment analysis?
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Great Question 12 months ago, created a question with more than 5,000 views. For Paired End Trimmomatic producing asymmetric paired read files.
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Popular Question 18 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
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