Tag: ignoreTxVersion

geneiD-genetranscript annotations

Hello, Trying to generate a frame with 2 columns: transcript_id and gene_id, in LINUX (gtf from esembl) grep -P -o ‘ESNCAGd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecag.txt grep -P -o ‘ESNCATd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecat.txt wc -l enseca* # To see if both files have the same length They are not the same length:…

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When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?

Hello, I’m working through my first batch of RNA-Seq analysis and unfortunately I don’t have an experienced bioinformatician to work with. My question is regarding tximport of my quant.sf files into R. I have been working with the EquCab3.0 reference transcriptome from NCBI to generate these quant.sf files, but I…

Continue Reading When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?