Tag: quant.sf

Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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Using salmon in Galaxy

Hi everyone. I am executing Salmon in Galaxy in order to carry out gene quantification from mouse RNA-Seq data (6 samples). To do so, I am providing a reference genome (cDNA, in fasta format), the processed reads (in fastqsanger.gz format) of one of these samples (after executing Trim-Galore) and a…

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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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deseq2 machine sizing best practices for very large data set

deseq2 machine sizing best practices for very large data set 0 @aa611017 Last seen 8 hours ago United States I want to perform differential expression analysis on a data set containing 17,000 samples. The salmon quant.sf files are about 1.5 Tb. based on my naive understanding of R and R…

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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…

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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…

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