Tag: bulkRNAseq

Bioconductor BulkRNAseq

Comment: deseq2 filter the low counts by Michael Love 40k You can’t filter the groups separately, you need to use a non-specific filter that doesn’t make use of information about which samples are … Comment: deseq2 filter the low counts by daiane.hemerichbrennan • 0 Hi Michael, I have another question…

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How do mRNASeq, BulkRNASeq, and TotalRNASeq differ in terms of workflow?

How do mRNASeq, BulkRNASeq, and TotalRNASeq differ in terms of workflow? 0 I want to look for differential gene expression a dataset from a collaborating lab. I have successfully done end-to-end analysis for mRNASeq, CHIPSeq and ATACSeq but I’m very confused about analyzing BulkRNASeq and TotalRNASeq. How different is the…

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CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM

CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM 0 Hi, I have bulkRNAseq dates (12 samples, pair end sequenced) and my pipine was : I performed quality control with FastqQC, Trimmed reads with Trimmomatic Aligned reads to the reference genome with STAR Used Samtools to sort and index the BAM…

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Batch effect consideration (re-seq the same sample twice)

Batch effect consideration (re-seq the same sample twice) 1 Hello, I would like to know how you guys address batch effects on re sequence on the same samples (Fastq files). Our client targeted 20 million reads for all of her samples. However, in the first run, we generated less than…

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Differential Gene Expression analysis in Bulk RNA Seq

Differential Gene Expression analysis in Bulk RNA Seq – using Count Matrix as input 1 Hello everyone, I am going to do the differential gene expression (DEG) analysis in the bulk RNA seq data. The sample used are the NAFLD samples downloaded from the NCBI Gene Expression Omnibus (GEO) (link…

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Bulk RNA seq with deseq2, rnaseqGene, or edgeR

Bulk RNA seq with deseq2, rnaseqGene, or edgeR 0 @fdd03415 Last seen 1 day ago United States Hi, This might be a very simple question but I am new to bulkRNAseq and would like to analyze paired FastQ files with DESeq2, rnaseqGene, or edgeR. Could anyone provide me with some…

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mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

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DEGs with uninsteresed sample files

DEGs with uninsteresed sample files 1 Hi all, I am working on some bulkRNAseq data from GEO and my sample description looks like this. I am interested in A vs B, A vs C and B vs C but I am not interested in sample D. My question is whether…

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