Tag: quant.sf

Effect of Bootstrapping/Gibbs Sampling in Salmon Counts 2 Hi Everyone, I am a bit confused about the difference between Gibbs Sampling and Bootstrapping when it comes to Salmon and how these procedures affect downstream analysis. For context, I am trying to do analysis of 49 matched cancer vs. normal RNAseq…

Good afternoon, I am trying to do a DTU analysis for my research, but I am kinda new to this stuff and I have some problems. In particular on point 5). I am following the workflow of Bioconductor vignette rnaseqDTU and my pipeline is this: 1) read salmon quants ##…

Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…

Now write an R script with the contents shown below to import the Salmon alignments into `DESeq2` and perform differential expression analysis. As with the previous script, since I provide the complete script, look up each of the functions used and make sure you understand how they are used here….

Salmon and SPAdes contigs filtering 0 Hello! I have a bunch of reference contigs, obtained with SPAdes, and RNA-seq data analyzed with salmon for control and experimental sample (let it be c_ and 2_). For every gene, there are several contigs, differing by length. Here are some tables Control: ~$…

when i trying import a list of salmon counts files quant.sf: txi <- tximport(files=files, type=”salmon”, tx2gene=tx2gene[,c(“refseq”, “entrezid”)], countsFromAbundance=”lengthScaledTPM”) Rstudio throw me a error: reading in files with read_tsv 1 Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : bad value why did it happen? Here are files…

Hi! I’m trying to do RNA-seq analysis using salmon and would like to have a matrix of read counts of 10 RNA fastq files. I installed salmon with bioconda, however, I can only find version : 0.8.1 even after ‘conda update salmon’. So I have been doing with version 0.8.1…

How to combine only reads columns from 6 different NM transcript ID based quant.sf files 1 Hello, Being beginner, I want to just know what is the simplest way to combine only read columns from 6 different NM transcript based quant.sf files. These transcript belongs to sheep and I want…

RNAseq Salmon (rnaseq_salmon)  is a DNAnexus Workflow that combines the two DNAnexus applets Salmon Scatter-Process-Gather Workflow  and quant_sf2express_table. Salmon Scatter-Process-Gather Workflow (salmon_spg_wf) is a DNAnexus applet that process a batch of pair-end FASTQ read files and runs Salmon to produce expression count files. quant_sf2express_table is a DNAnexus applet that generates expression table files suitable for RNA-seq Expression…

How to solve, Error, the column headings: are not unique. in Build Transcript and Gene Expression Matrices 0 I’m trying to generate Build Transcript and Gene Expression Matrices, my command is: /trinityrnaseq-v2.13.2/util/abundance_estimates_to_matrix.pl –est_method salmon Sy_Externa_1/quant.sf Sy_Externa_2/quant.sf Sy_Externa_3/quant.sf Sy_Externa_4/quant.sf Sy_Externa_5/quant.sf Sy_Externa_6/quant.sf Sy_Externa_7/quant.sf Sy_Interna_1/quant.sf Sy_Interna_2/quant.sf Sy_Externa_3/quant.sf Sy_Externa_4/quant.sf –gene_trans_map none –name_sample_by_basedir * Outputting…

Salmon TPM calculation constant 1 Hi all, salmon seems to calculate the TPM using the equation below, and looks like the constant is 26.1 for every calculated TPM. Does anybody know what this constant means and how it’s derived? TPM = constant * NumReads / EffectiveLength, salmon TPM • 44…

Hello, Apologies for a pretty elementary question. I tried my best to answer it using resources online but I find many tutorials/explanations out there difficult to understand. I am trying to quantify human rnaseq data using salmon. The reason I am using salmon is because I would like to perform…

Import quant.sf files 0 Hi, I have a problem in importing quant.sf files. I’ve already read a lot of posts, but I can’t solve the issue. I have ~600 quant.sf files obtained from Dragen RNA analysis and they are all in the same folder. I would like to import them…

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…

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…

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…

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…

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…

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…