Tag: quant.sf

python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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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?

How do I match my transcript ID’s from NCBI to the corresponding gene ID’s to enable tximport into R?

How do I match my transcript ID’s from NCBI to the corresponding gene ID’s to enable tximport into R? 2 Hi all, New to RNA-Seq analysis and I tried to find an answer to this elsewhere. I have performed salmon alignment on my pair-end fastq files which has generated the…

Continue Reading How do I match my transcript ID’s from NCBI to the corresponding gene ID’s to enable tximport into R?