Tag: Rsubread
multi-mapping reads settings in Rsubread or Rsubjunc
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…
Potential segfault bug in featureCounts using long read data
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
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
“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…
Correct script for featurecounts in Rsubread
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
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,…
Error generating counts df for use with DRIMSeq/DEXseq
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…
featureCounts with NCBI T2T not capturing all genes
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…
conda create env using .yml file leads to dependency conflicts
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…
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
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…
Bioconductor – samExploreR
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
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
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…
Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs
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….
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
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
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…
Index of /Rsubread/annot
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
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
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,…
Accepted r-bioc-rsubread 2.10.0-1 (source) into unstable
—–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)
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
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…
Bioconductor – Rsubread
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,…
Accepted r-bioc-rsubread 2.8.2-1 (source) into unstable
—–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:…
Error in Rsubread featureCounts
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: ========== _____ _ _ ____ _____ ______…
Aligning multiple single and paired-end reads from multiple files (lanes)
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”
“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…
Rsubread align maximum nthreads
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…
