gene_id in ENCODE dataset

Hi,

I have downloaded the RNA-seq dataset from https://www.encodeproject.org/experiments/ENCSR000CGV/ .

My objective is to look at the expression of few hundred genes in this dataset. However, I dont know how to convert the gene_id here to gene name.

I am not sure if I can use biomaRt package in R, because there is not gene_id in the listAttributes output.

Find Image here

Thanks

encode rna-seq rna-seq

• 1,291 views • link

written 8.4 years ago by evocanres •

0 answers

No answers yet.

More posts like this

low quality data or file name swapping -- cellranger arc errors when processing 10x scMultiomics da…
written 8 months ago by Wu-Sheng Zhang •

I downloaded scMultiomics data from [here](https://www.encodeproject.org/multiomics-series/ENCSR128ZLB/). To be specific, I downloaded snATAC-seq from [here](https://www.encodeproject.org/experiments/ENCSR083HFN/). I made an ATAC folder and downloaded all snATAC-seq files to …
Choosing the "right" sequence as an input control
written 1.4 years ago by mark.pekarsky •

Hello everyone, when I am looking for sequences for ChIPseq analysis, there are usually multiple links, for example, for the control sequences. https://www.encodeproject.org/experiments/ENCSR792GCH/ So which …
ERROR When Using Ensembl Plants Biomart Wget API
written 2.3 years ago by Dora •

I am going to use wget to download data from ensembl plants biomart By following the instruction here: [https://plants.ensembl.org/info/data/biomart/biomart_restful.html#biomartperlapi][1] I use this command: ``wget -O …
Can't convert dog ensembl IDs into gene names
written 4.6 years ago by fifty_fifty •

I usually use biomaRt to convert gene ids to symbols. However, this time the ensembl IDs I have (dog) do not match the ensembl ids …
biomaRt does not convert entrez gene id to ensembl gene id
written 5.1 years ago by Bane •

I am trying to convert my entrez gene_id to ensembl gene_id. Here is my R codes ---------- > library(biomaRt) > ensembl<- useEnsemblGenomes(biomart = "plants_mart") > …
FeatureCounts Output contains gene_id or transcript_id?
written 5.1 years ago by Bane •

Hello! 1 month ago i completed a transcriptome study. While making the normalization step, i used featurecounts. My featurecounts code was; >featureCounts -a Beta_vulgaris_ncbi.gtf -g …
biomart returns several ensembl ids for one gene
written 5.3 years ago by fifty_fifty •

I have to convert the gene names in my scRNA-seq data into ensembl IDs for downstream analyses. I used biomaRt package which converted some of …
biomaRt not finding all genes
written 5.7 years ago by danielcgingerich •

I need to align a dataset mapped to GRCh38.p2 (ensembl 79) and a dataset mapped to GRCh38.p13 (ensembl 98). The first dataset (ensembl 79) has …
Different filters for wheat in biomaRt package and website
written 7.5 years ago by sandeep.amberkar18

Hello, I'm looking to download the Wheat TILLING & SNP data from Ensembl from the biomaRt package in Bioconductor. However, I've noticed that the filters …
What kind of accession code is NP_000123.1?
written 11.6 years ago by Good Gravy •

I am batch retrieving a few hundred codes that vary slightly in length and sometimes have XP rather than NP. In uniprot, from the dropdown …