Tag: smallRNA

invalid deflate data (invalid code lengths set)

I am trying to trim paired end reads using Trim-Galore. I have made sure that the files match based on the total reads processed in the output txt file from trim-galore. One of the files trimmed correctly but when I try some of the others the total written and quality…

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small RNAseq analysis of non human samples

small RNAseq analysis of non human samples 0 Hello all, Please share a workflow/pipeline for RNAseq analysis focused on small RNA of insects such as roaches. Since annotation is available for protein coding only, in this scenario how do i deal with question of regulation of small RNA Any help…

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Bioconductor MicroRNAArrayData

Comment: why is downloading the .tar.gz file for a given bioconductor package, then insta by Ndimensional ▴ 20 Sorry about the N=2. That was meant to read 20 (following the 10 in the previous sentence), my apologies there. The provided link to MSMB-… Answer: smallRNA-seq analysis batch correction in limma…

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smallRNA-seq analysis batch correction in limma

Good morning, I am currently trying to analyse a small-RNA sequencing dataset using limma package and the voomLmFit function. However, I am experiencing some issues with the p-value distribution, with some of the comparisons I am testing showing odd p-value distribution. This probably indicates that there is some kind of…

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Babraham Bioinformatics – FastQC A Quality Control tool for High Throughput Sequence Data

FastQC Function AMPERE quality control tool for elevated throughput sequence data. Your Java What A match Java Runtime Ecology This Picard BAM/SAM Libraries (included in download) Code Maturation Robust. Mature code, but feedback exists comprehended. Code Released No, under GPL v3 or later. Initial Contact Simon Andrews Download Now Views…

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Use of DESeq given unusual experimental data

Use of DESeq given unusual experimental data 0 @glfreynolds-21471 Last seen 13 hours ago United Kingdom Hello, I’ve been using DESeq for some smallRNA-seq I’m working on, but we have some unusual data given what we’re sampling the small RNA-seq data from (sorry to be cryptic, I’m bound by confidentially…

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small RNA Workflow

small RNA Workflow 1 Hello World ! Looking forward a solution reagarding choosing best small RNA workflows(pre-processing->results/reports) based on following perspectives Execution Mode : Linux based, Standalone with command line mode. Not web-based. Organism : Insects Based on reviews : mimiARma-Seq | The UEA sRNA Workbench | SePIA | CAP-miRSeq…

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small RNA sequencing

small RNA sequencing 0 Hello everyone, I have paired end small RNA seq raw data. I have to differential expression analysis. Can anyone help me how to start it? Thanks smallRNA Sequencing • 77 views • link updated 2 hours ago by Buffo ★ 2.0k • written 12 hours ago…

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Error in DESeqDataSetFromHTSeqCount

I am using HTseq pipeline for DESeq2: Directory = “/Users/abhaykanodia/Desktop/smallRNA/” condition = c(“WT1”, “WT2”, “WT3”, “NTC1”, “NTC2”, “NTC3) sampleFiles= c(“AK1a_counts.txt”,”AK2a_counts.txt”,”AK3a_counts.txt”,” AK4a_counts.txt”,”AK5a_counts.txt”,”AK6a_counts.txt”) sampleName = c(“AK1”, “AK2”, “AK3”, “AK4”, “AK5”, “AK6”) sampleTable <- data.frame(sampleName = sampleName, fileName = sampleFiles, condition = condition) sampleTable The output is: sampleName fileName condition 1 AK1 AK1a_counts.txt…

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smallRNA profiling using HTSeq error

smallRNA profiling using HTSeq error 1 Hello, I want to create a “count” file using HTseq. I have both BAM file and gtf file: htseq-count -f bam -s no -i AK1a_clean_Aligned.sortedByCoord.out.bam gencode.v42.chr_patch_hapl_scaff.annotation.gtf >> AK1a_counts.txt It still gives an error: htseq-count: error: the following arguments are required: featuresfilename Can someone please…

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Standard for aligning smallRNA to a reference human rRNA?

Standard for aligning smallRNA to a reference human rRNA? 0 Hi, I need to label some smallRNA sequences that I know are rRNA fragments. I know that for mRNA these are discarded by aligning to the human genome and filtering out multimapped reads, but I need to try to pin…

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tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics

tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is a graphical user interface (GUI) tool for the analysis of tRNA expression profiles from deep-sequencing data of small RNAs (small RNA-seq) using R packages. The whole analysis workflow, including the uploading of FASTQ files of small RNA-seq, quantification of…

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Bioconductor – mirTarRnaSeq

DOI: 10.18129/B9.bioc.mirTarRnaSeq     mirTarRnaSeq Bioconductor version: Release (3.14) mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis…

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small dimensions in the matrix of counts from smallRNA using DESEq2

small dimensions in the matrix of counts from smallRNA using DESEq2 1 @andreia-23745 Last seen 8 hours ago Portugal Hi there, I am doing smallRNA data analysis and I have a matrix of counts 17 miRNA and 16 samples I wonder if its correct to perform the results() from DESeq2…

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how to use old and new smallRNAseq data sets for data analysis

how to use old and new smallRNAseq data sets for data analysis 0 I have some smallRNAseq data (already sequenced) and would like to generate smallRNAseq from another few samples. but at the end I would like to include both new and old batches in the data analysis. For smallRNA…

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