User: vujex

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vujex0
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Posts by vujex

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htseqcount missing mates
... Hello I'm having a hard time understanding the behaviour of HTSeqcount. I first sorted my bam files: `samtools sort sample1.bam > sample1_sorted.bam` Then I ran: `htseq-count -f bam -m intersection-strict -s no -a 10 -t gene -i gene_id sample1_sorted.bam file.gff3 > sample1_count.txt` And ...
samtools htseqcount written 3 months ago by vujex0 • updated 7 weeks ago by Biostar ♦♦ 20
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from WGCNA to cytoscape
... Hello I am working with RStudio/WGCNA to make co-expression networks from RNA-seq data (40 samples and 4000 genes). I succeeded at making the similarity and adjacency matrixes now I did the following to cluster my data (and it worked) `tree <- hclust(as.dist(1 - adj.mat), method="average") ` ...
wgcna cytoscape export written 3 months ago by vujex0
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Comment: C: Best method for phylogeny on bacterial genes
... Thanks! I have DNA data so don't think I can use PMSF. I did however use GTR made 40 trees and took a consensus using IQ-TREE command (iqtree -con mytrees -minsup 0.5). The result looks dodgy and not biologically meaningful but this could be caused by the dataset. ...
written 3 months ago by vujex0
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Comment: C: How to concatenate multiple fasta file
... Hi, I am having the same question as this one. But my headers look different, I tried your solution but it removes all of my headers. Would you be so kind to help me with it? >Lineage-1-Name-L1 ATGCGGAAAGGGGTTGATCTCGTGACgGC.... >Lineage-2-y2007-018 ATGCGGAAAGGGGTTGATCTCGTGACg ...
written 3 months ago by vujex0
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Best method for phylogeny on bacterial genes
... Hello! I have approximately bacterial 40 (non conserved) genes in which I am interested, I want to build a phylogenetic tree per gene (so 40 trees) and later I want to (try) take a consensus tree of that. All of the genes are around 200-500bp. I have installed raxml, iqtree and megax, and I can wor ...
phylogeny raxml iqtree megax written 4 months ago by vujex0 • updated 3 months ago by Lesley Sitter540

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