Tag: Rsubread

Hello everyone, I am stuck trying to analyze some single-end RNAseq data from human tissue. My issue is that the alignment with HISAT 2 went very well: 94.95% overall alignment rate. However, when I use featureCounts, I get: 5.7% when I set the strandSpecific parameter to 1. 5.3% when I…

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Parent directory/ – – r-bioc-rsubread_2.12.2-1.debian.tar.xz 3.9 KiB 2022-Dec-20 05:29 r-bioc-rsubread_2.12.2-1.dsc 2.0 KiB 2022-Dec-20 05:29 r-bioc-rsubread_2.12.2-1_amd64.deb 10.2 MiB 2022-Dec-20 05:56 r-bioc-rsubread_2.12.2.orig.tar.gz 12.8 MiB 2022-Dec-20 05:29 r-bioc-rsubread_2.14.2-1.debian.tar.xz 4.0 KiB 2023-Jul-20 11:19 r-bioc-rsubread_2.14.2-1.dsc 2.0 KiB 2023-Jul-20 11:19 r-bioc-rsubread_2.14.2-1_amd64.deb 10.2 MiB 2023-Jul-20 11:54 r-bioc-rsubread_2.14.2.orig.tar.gz 12.8 MiB 2023-Jul-20…

Dear community, I have been struggling finding the problem for the past few days now. I work on making a differential expression analysis (DEA) with direct RNA nanopore long reads from the minion platform. I ran into this wall and I would really appreciate your help! I sequenced the RNA…

Dear community, i have been struggling finding the problem for the past few days now. I work on making a differential expression analysis (DEA) with direct RNA nanopore long reads from the minion platform. I ran into this wall and i would really appreciate your help! I sequenced the RNA…

I am aligning RNA-seq data to a custom reference using subjunc(): align.res <- subjunc(index=”Repvec”, file1=fwdname, readfile2=revname, output_file=bamname, nthreads = 6, sortReadsByCoordinates=TRUE) With the last parameter, the BAM file is sorted and the .bai file is created. Everthing is fine, when I load the BAM file into an genome viewer; however,…

RSubread DESeq2 0 Hi everyone, I am new in bioinformatics and when I try to use DESeq2 for my counts and further downstream analysis, I am faced with this problem. dds <- DESeqDataSetFromMatrix(countData = count_matrix, colData = NULL, tidy = TRUE) Error in rownames<-(*tmp*, value = colnames(countData)) : attempt to…

This post is in response to a number of emails and posts asking about reading data into edgeR and producing RPKM. Suppose we start with a tab-delimited file counts.txt like this: To read this into edgeR: library(edgeR) Data <- read.delim(“counts.txt”, sep=”\t”, row.names=1) y <- DGEList(Data, annotation=”Length”) To normalize the library…

MenAT1 sequence analysis Analysis of gene neighbourhoods for rv0078B (menA1) was performed using default settings in FlaGs (www.webflags.se/). Output sequences for MenA1 and cognate MenT1 homologues were then used to perform sequence alignments using MUSCLE (www.ebi.ac.uk/Tools/msa/muscle/), then formatted in Jalview (www.jalview.org/), sorting by pairwise alignment. Residues of interest were then…

DOI: 10.18129/B9.bioc.autonomics   Generifying and intuifying cross-platform omics analysis Bioconductor version: Release (3.17) This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm. Author: Aditya Bhagwat…

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‘Killed’ error during RNAseq alignment 1 @fea7fd29 Last seen 8 hours ago India I am trying to align RNA sequencing data using the following code. However, it shows an error killed at the end. It does not specify the reason as well. I initially assumed memory could have been an…

Obtain counts for specific genes with ChIP-seq data without peak calling 1 Hello, I was wondering if it is possible to obtain counts for an specific set of genes without doing peak calling. The idea will be to perform an alignment and then obtain the counts for the set of…

multi-mapping reads settings in Rsubread or Rsubjunc 0 Hi All, I am using Rsubjunc to process my RNA seq data for DEseq2 and differential splicing analysis. I have a question about how to set multi-mapping reads alignment in Rsubjunc R package. The command I used is attached to the end…

Hi, I think I might have found a bug in featureCounts from Rsubread (v2.12.3). I am trying to find reads overlapping exon junctions from a personalised reference, using Nanopore long read BAMs. I am afraid I cannot share fully reproducible code as I am using my own reference, but this…

Download stats for annotation package Rsubread This page was generated on 2023-04-20 08:18:02 -0400 (Thu, 20 Apr 2023). Rsubread home page: release version, devel version. Number of downloads for annotation package Rsubread, year by year, from 2023 back to 2009 (years with no downloads are omitted): 2022 Month Nb of distinct IPs Nb of downloads…

“align” in rsubread only reading 1 out of 6 of my input files 1 Hi all, I’m trying to align 6 rnaseq fastq.gz files to the index i just build using rsubread, but every time I run the command ” align(index=”zfish_index”, readfile1= readfile1, readfile2=NULL, type= “rna”, input_format=”gzFASTQ”,output_format=”BAM”) ” (readfile1 is…

I am new to R and RStudio but have been trying to work through different examples using Rsubread for my data. I have tried reading vignettes and manuals prior to posting here but I am stuck and could really use some advice. I have 7 paired-end, fastq files from Illumina…

Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file 2 Hello! I’ve de-novo assembled a transcriptome from Trinity, resulting into Trinity.fasta, whose headers look like this: >TRINITY_DN29256_c0_g1_i1 len=323 path=[0:0-322] Followed, in the next line, by the sequence. To run an external downstream analysis with a R script,…

Hi, I am attempting to work through the workflow described in “Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.” I am running into an error message when I try to make the counts dataframe for DRIMseq: Error in data.frame(gene_id = txdf$GENEID, feature_id = txdf$TXNAME, cts) : arguments…

Hello, My team would greatly appreciate assistance with running featureCounts using the human NCBI T2T assembly (assembly (T2T-CHM13v2.0) as a reference; when we run it we end up with nearly 14,000 fewer genes than what the annotation supposedly contains.What (if any) modifications can be made to run Subread or RSubread…

Hi all, I’m trying to create a conda environment through a .yml file that has all the required dependencies for a certain project but I run into environment conflicts. I figured out the source of this conflict, which stems from two specific dependencies, but for some reason, creating an environment…

Hi, I am new to Single cell analysis but have some experience with NGS data output and manipulation. I have a set of .bam that I assume were the product of the cell ranger pipeline from the ENA (project ID PRJEB36998) unfortunately I have no access to any other output…

DOI: 10.18129/B9.bioc.samExploreR     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see samExploreR. samExploreR…

Rsubread align every slow in mac but faster in windows 0 @a553f2ee Last seen 1 day ago United States I tried to use Rsubread to align a few thousands reads to a 1.5 kb reference, and tested in mac OS and windows with similar configuration. I found in mac took…

RNA-seq library size – significant sample discrepency 2 Hello, I’ve been given some data to perform differential expression on, and it the process of QCing the resultant count data, I’m seeing that the library sizes have pretty big discrepancies between the 2 samples shown below. I know a good run…

Ellis, E. C. et al. Anthropogenic transformation of the biomes, 1700 to 2000. Glob. Ecol. Biogeogr. 19(5), 589–606 (2010). Google Scholar  Soleimani, T., Hermesch, S. & Gilbert, H. Economic and environmental assessments of combined genetics and nutrition optimization strategies to improve the efficiency of sustainable pork production. J. Anim. Sci….

Hi, running Rsubread 2.8.2/2.12.0 or featureCounts 2.0.3/2.0.1, I stumbled over two issues when allowing ambiguous read assignment (-O/allowMultiOverlap) 1) regarding assignment via minimum fractional overlap (–fracOverlap) using featureCounts stand-alone binary. 2) when combined with –/largestOverlap and –/fraction using Rsubread featureCounts function or the stand-alone binary. to 1) Assume a read…

Rsubread featureCounts outputs dozens of temp files, no counts 1 @83165de1 Last seen 16 hours ago United States Hello, I am having trouble getting an output file in Rsubreads using featureCounts. I want to set up my data to run analysis of differential expresssion in EdgeR. I’m running about 40…

Name Last modified Size Description Parent Directory   –   chm13v2.0_RefSeqStri..> 2022-08-22 01:51 2.0M   chm13v2.0_RefSeq_12A..> 2022-08-22 01:51 2.5M   code/ 2022-08-22 01:53 –   hg38_RefSeqStrict_22..> 2022-08-22 01:51 2.3M   hg38_RefSeq_22Apr202..> 2022-08-22 01:51 3.0M   mm10_RefSeqStrict_22..> 2022-08-22 01:51 2.0M   mm10_RefSeq_22Jun202..> 2022-08-22 01:51 2.5M   mm39_RefSeqStrict_23..> 2022-08-22 01:51 1.9M  …

Rsubread featurecounts 1 Hi there, I seem to be getting this error when reading in a BAM file which was generated by PBMM2 align on pacbio data. I have tried to google the error message but there are no results. I wonder if anyone has ideas on what the error…

Using featureCounts and downloading Rsubread 1 @4769e097 Last seen 23 hours ago United Kingdom I am trying to perform a count per gene analysis using featureCounts in R. I have downloaded the gtf file and edited it within R to only contain the gene ID, chr, start, end, and strand,…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2022 14:00:29 +0200 Source: r-bioc-rsubread Architecture: source Version: 2.10.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-rsubread (2.10.0-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version:…

Annotated file with gene ID (instead of gene symbol) 0 @9cb59de3 Last seen 14 hours ago United States Hello, I am using “featureCounts” in Rsubread package for analyzing bulk RNA-seq of drosophila. Since there is no inbuilt annotations of drosophila, I am using a gtf file in the homepage of…

Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error 0 @efernandez-22025 Last seen 1 day ago Argentina Hi I am triying to build the human index using ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz I am using Rsubread 2.4.3 an it gives me the following error //================================= Running ==================================\ || || || Check the integrity of…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 21 Mar 2022 21:39:43 +0100 Source: r-bioc-rsubread Architecture: source Version: 2.8.2-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-rsubread (2.8.2-1) unstable; urgency=medium . * Team upload. * New upstream version * Maintainer:…

Hi there, Excellent package! I am using it to do RNA-seq. But I encountered a small problem when using featureCounts(). The code is as follows: featureCounts( “A1.raw_1.fastq.gz.subjunc.BAM”, annot.inbuilt = NULL, annot.ext = “GCF_015227675.2_mRatBN7.2_genomic.gtf”, isGTFAnnotationFile=TRUE, isPairedEnd=TRUE, nthreads = 8 ) And it returns this: ========== _____ _ _ ____ _____ ______…

Rsubread: Aligning multiple single and paired-end reads from multiple files (lanes) 0 Hello, I am new to bioinformatics and looking for some help. I have 27 files from an Illumina output. There are 4 paired end and 23 single read files. I am trying to align them using Rsubread in…

“Paired-end reads were detected in single-end read library” 0 @9cb59de3 Last seen 12 hours ago United States Hello, I am using “featureCounts” in Rsubread package for analyzing bulk RNA-seq of drosophila. Since there is no inbuilt annotations of drosophila, I am trying to use a gtf file in the homepage…

Hi Experts, I am using Rsubread align using following comand- align (index=”my_index”, readfile1 = “SRR123456_1.fastq” ,readfile2= “SRR123456_2.fastq”, type=”rna”,input_format = “FASTQ”, minFragLength=35,maxFragLength=151,useAnnotation=”TRUE”, nthreads=64, annot.ext = “my_annotation.gtf.gz”, isGTF = “TRUE”, sortReadsByCoordinates = “TRUE”, output_format = “BAM”) here i have asigned 64 threads but in console, i see only 40 threads, I dont…