User: dimitrischat

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dimitrischat70
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Posts by dimitrischat

<prev • 80 results • page 1 of 8 • next >
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GOplot GOcluster plots
... Hello all. I ve been trying to do some plots from GOplots in R. But i have some issues regarding GOcluster GOheat and GOVenn. With GOcluster (myprocess file is names of GO): > GOCluster(circ, myProcess, clust.by = 'logFC', term.width = 2) i get an error >ERROR Error in stats::hclust(dista ...
rna-seq written 7 weeks ago by dimitrischat70
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Comment: C: Circos:- How To Make Circos Histogram Image Using This Data
... can anyone explain to me how do i get all the 4 columns (from bed files i dont have the 4th -value) ? for example from a bigwig file ? ...
written 9 weeks ago by dimitrischat70
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Answer: A: GOplot - tutorial
... From what i can see from EC$genelist it requires these columns > ID logFC AveExpr t P.Value adj.P.Val B But i got > id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj What is AveExpr t and B compared to my data? (also i dont know what is "t" and "B") obviously logFC = l ...
written 3 months ago by dimitrischat70
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Comment: C: hicexplorer hicPlotTADs configuration file
... yes, just some clarification needed. ...
written 3 months ago by dimitrischat70
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hicexplorer hicPlotTADs configuration file
... Wanted to ask about the configuration file .ini that you have to put as input for the hicPlotTAD tool. First of you create it yourself using f.e. text editor and save it as .ini file ? Also you must have this configuration file among the .h5 .bed .bw files that are in the configuration file or it do ...
chip-seq written 3 months ago by dimitrischat70 • updated 8 weeks ago by Biostar ♦♦ 20
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GOplot - tutorial
... Hi all, I am new in R and bioinformatics and i wanted to know what are the steps to prepare data for the R package - GOplot. I ve read the tutorial here : http://wencke.github.io/ , installed all packages needed. But i dont know how to prepare my data so i can import them into the R package and also ...
rna-seq written 3 months ago by dimitrischat70
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Answer: A: How to subset a bed or gtf file to some genes of interest?
... I got a similar question for this, because grep -f or grep -F doesnt work for me. I got a list of common genes between two cell types. Now i want to pick only the common genes from each condition ( each cell type ) from an excel file that contains id baseMean baseMeanA baseMeanB fold ...
written 3 months ago by dimitrischat70
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Comment: C: STAR fusion error
... it made a difference..it worked for a long time till reported other error. I searched inside the genome resource library foder and i cant find that file(that reports the error) : "ref_annot.gtf" , but there are : "ref_annot.gtf.gene_spans" , "ref_annot.gtf.mini.sortu" . By the way this is the plug ...
written 3 months ago by dimitrischat70
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Comment: C: STAR fusion error
... i force installed the 2.6.1d so now it works. Also i downloaded the plug and play genome resource library so i guess thats ok. My command is : STAR-Fusion --left_fq GlentisS1_S17_R1_001.fastq.gz --right_fq GlentisS1_S17_R2_001.fastq.gz --genome_lib_dir '/..../GRCh38_v27_CTAT_lib_Feb092018/ctat_ ...
written 3 months ago by dimitrischat70
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Comment: C: STAR fusion error
... thanks a lot. I installed it like you said. But when i type : > conda activate star-fusion nothing happens. I also tried after activating enviroment : > star-fusion but still nothing ...
written 3 months ago by dimitrischat70

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Popular Question 4 months ago, created a question with more than 1,000 views. For from txt to bed
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