User: 2405592M

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2405592M40
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Posts by 2405592M

<prev • 24 results • page 1 of 3 • next >
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weird python error
... Hi people! I downloaded this [program][1] and I'm trying to generate a tRNA database but I keep getting the following error: Traceback (most recent call last): File "maketrnadb.py", line 73, in getmaturetrnas.main(trnascan=[scanfile], genome=genomefile,gtrnafa=gtrnafafile,bedf ...
python oserror written 8 weeks ago by 2405592M40 • updated 8 weeks ago by bioinformatics202030
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multiple comparisons in DESeq2
... Hi guys, I have the following sample information table I'm using in DESeq2: FileName Sample Condition Day 1 WT_2_Aligned.sortedByCoord.out.bam WT_2 WT Uninduced 2 WT_3_Aligned.sortedByCoord.out.bam ...
deseq2 rna-seq written 11 weeks ago by 2405592M40 • updated 11 weeks ago by swbarnes27.2k
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Comment: C: How can I get Ensembl CDS / 3'UTR and 5'UTR sequences
... Hi Emily, I'm trying to do this through R using the following: library(biomaRt) listMarts() ensembl <- useMart("ensembl") datasets <- listDatasets(ensembl) head(datasets) ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl) at ...
written 11 weeks ago by 2405592M40
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How can I get Ensembl CDS / 3'UTR and 5'UTR sequences
... Hi all, I've finished doing an RNA-seq analysis and I've done some differential expression on my data set. I now want to do some codon usage analysis between conditions for my up and down regulated genes. How can one get the 3'UTR / CDS / 5'UTR sequences with ensembl IDs? Thanks in advance! ...
ensembl sequence rna-seq codon usage written 11 weeks ago by 2405592M40 • updated 11 weeks ago by Emily_Ensembl20k
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Comment: C: Dealing with ensembl gene ID and enterez ID duplicates
... After further inspection, I have do have ensembl duplicates but this is because I have multiple enterez IDs for the same ensembl ID ... should I concatenate the multiple enterez IDs. Also, If I just accepted one of the enterez IDs and discarded the duplicates would I lose data? I'm currently under t ...
written 11 weeks ago by 2405592M40
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Dealing with ensembl gene ID and enterez ID duplicates
... Hi Guys, I have done some differential expression analysis on some RNA-seq data (counts were mapped to the genome) and I am satisfied with the results (examined briefly by looking for the downregulation of my knockout gene and its associated interactome). I then attempted to put together a spreads ...
annotation deseq2 rna-seq written 12 weeks ago by 2405592M40
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Comment: C: What is the gold standard for the one-to-many relationships in BioMart retrieved
... Hi Mike, Thank you for your reply. My counts and differential expression are both gene based and yes, indeed the specific transcripts based on biotype etc are not needed in my analysis. I simply want to annotate my dataset and add entrez IDs so I can do GSEA/KEGG which from my understanding, need ...
written 12 weeks ago by 2405592M40
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What is the gold standard for the one-to-many relationships in BioMart retrieved annotations and adding them to a DESeq2 results table
... Hey guys, I've done differential expression analysis on an RNA-seq experiment using DESeq2 and I now want to add my BioMart annotations to my DESeq2 results table. I've selected my BioMart database and generated an annotation using: ensembl <- useMart("ensembl") datasets <- li ...
one-to-many relationships biomart deseq2 written 5 months ago by 2405592M40 • updated 5 months ago by Mike Smith1.4k
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Comment: C: Trouble manipulating dataset
... Perfect! Aggregate was the function I needed! Cheers! ...
written 8 months ago by 2405592M40
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Trouble manipulating dataset
... Hi Guys, I'm having trouble with some data manipulation. I have the following table where I have the raw counts from an RNA-seq experiment. I'm trying to group all my counts by tRNA wobble position. head(df) Isodecoder Anticodon Wobble Loci Fragment_type AAV_Ctrl1 AAV_Ctrl2 AAV_Ctrl3 AAV_Cre1 ...
R rna-seq written 8 months ago by 2405592M40 • updated 8 months ago by shawn.w.foley1.1k

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