Tag: ignoreTxVersion

Batch and Sample correction for downstream analysis using DESeq2

Hello everyone, I am an absolute beginner on sequencing analysis and DESeq2, so please forgive me for possibly mundane questions. I have tried to look up different methods, but couldn’t find a fitting answer yet. I am currently working with sequencing data derived from an Illumina sequencer. The data is…

Continue Reading Batch and Sample correction for downstream analysis using DESeq2

How to properly compare the group-specific samples using DEseq2

I am trying to analyze the RNAseq data using Salmon + DEseq2. I have two variables: genotype (WT or KO) + condition ( treatment A or B), as shown below: >samples # run genotype condition #sample1 sample0001_quant WT A #sample2 sample0002_quant WT B #sample3 sample0003_quant KO A #sample4 sample0004_quant KO…

Continue Reading How to properly compare the group-specific samples using DEseq2

error with Tximport when txOut = TRUE

Hello everyone, Hello Everyone, I am having issue with when trying to aggregate transcript abundances to the gene level (when txOut=FALSE) but it works fine with txOut=TRUE. Here are the steps I followed: Produced bam file using Gencode transcript fasta file. Further sorted and index them. Used Nanocount to produce…

Continue Reading error with Tximport when txOut = TRUE

kallisto + GENCODE transcript sanitization

Hi all, I ran into an edge case situation of kallisto not processing GENCODE transcript identifiers correctly, and this currently propagates into tximport. Ideally this should be fixed upstream in kallisto, but we should harden tximport against this situation. Here’s an example kallisto run aligned against GENCODE that is problematic:…

Continue Reading kallisto + GENCODE transcript sanitization

Problem with tximport and plasmodium falciparum

Hello, I aligned my samples with kallisto to a transcriptome for plasmodium falciparum. The file I used to make the reference is Plasmodium_falciparum.ASM276v2.cdna.all.fa.gz which I downloaded from here ftp.ensemblgenomes.org/pub/protists/release55/fasta/plasmodium_falciparum/cdna/Plasmodium_falciparum.ASM276v2.cdna.all.fa.gz. However, I am having issues with tximport. The error that I get is: Error in .local(object, …) : None of the…

Continue Reading Problem with tximport and plasmodium falciparum

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:…

Continue Reading geneiD-genetranscript annotations

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?