Question: Could not find rRNA genes (28S, 18S, 5.8S and 5S) in human_genes.gtf file?
0
gravatar for bioinforesearchquestions
2.7 years ago by
United States
bioinforesearchquestions140 wrote:

Dear All,

 

I am searching for human 28S, 18S, 5.8S and 5S rRNA (RNA28S, RNA18S, RNA5-8S and RNA5S genes) and also 12S and 16S mitochondrial rRNA (MT-RNR1 and MT-RNR2) in human_genes.gtf file from UCSC. 

I am unable to find these genes(RNA28S, RNA18S, RNA5-8S, RNA5S, MT-RNR1 and MT-RNR2 genes) in human_genes.gtf file. I am looking at gene_id or gene_name in gtf file.

How do I check these genes in gtf file or in any other resources.

Is it saved in some other name?

 

 

 

rrna genes rna-seq gtf file gene • 1.6k views
ADD COMMENTlink modified 2.7 years ago by Devon Ryan81k • written 2.7 years ago by bioinforesearchquestions140
1

You can try to looking for in GENCODE resources. ;)

ADD REPLYlink written 2.7 years ago by glihm560
1
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

You can find 5S, 5.8S and MT_rRNA in the Ensembl/Gencode files. The others aren't in the reference genome (they're on an unplaced contig). If you need the sequences then you can get them from NCBI (the ones not in the reference genome come from 45S).

ADD COMMENTlink written 2.7 years ago by Devon Ryan81k

Thanks Devon. I am using new kit which is expected to remove eukaryotic cytoplasmic rRNA, mitochondrial rRNA. In order to know the reads associated to these rRNA genes. I have the output from htseq-count. Only RNA5-8S5 alone is found in human_genes.gtf file and also in htseq output. Then how do I get the numbers of reads for other rRNA genes.

ADD REPLYlink written 2.7 years ago by bioinforesearchquestions140

You might download the 45S sequence that I linked to, add it to your genome, and then map to that. Just add a line to the GTF file including either that whole contig or each of the constituent parts (the bounds of 28S and so on are noted on the NCBI site).

ADD REPLYlink written 2.7 years ago by Devon Ryan81k

I downloaded the hg19 whole genome fast sequence from UCSC. I built the bowtie2 index file based on the whole genome. I have a doubt here, then the 45S rRNA sequence is not present in the whole genome sequence file. 

ADD REPLYlink written 2.7 years ago by bioinforesearchquestions140

I know, that's why I said to add the sequence from NCBI to it.

ADD REPLYlink written 2.7 years ago by Devon Ryan81k
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