Tag: HT-Seq

Patrick Murphy Bulk RNA-Seq – HackMD

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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HT-Seq, Gene ID appeared in Gene Name row

HT-Seq, Gene ID appeared in Gene Name row 0 Hi, I am doing alignment with HISAT2 and couting with HT-seq. I got the counting matrix but i found there are gene ID appear in the gene name row. Is it normal that gene ID can appear like this or are…

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RNA Seq HTSeq download GDC portal

RNA Seq HTSeq download GDC portal 0 Hi friends, I am trying to download ht-seq file form GDC portal but it gives me one file for each patinets. Can you please let me know how to download one file including all patients together for all 60000 genes? Is there any…

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RNASeq deseq2

RNASeq deseq2 1 Hi friends I have RNASeq data fromTCGA as HT-seq format. I want to do Deseq2. some patient names are duplicated and deseq2 dose not accept them. How would I deal with the duplicated patients? deseq2 RNASeq • 229 views • link 1 day ago by Rob ▴…

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GSVA R packages

GSVA R packages 1 Hello everyone, I’m trying to do a gene set varian analysis using R to detect a specific gene set signature of a specific pathway from 20 samples of RNA-seq. I have this files in BAM format but I don’t know what to do in order to…

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