how can i download human ribosomal reference ?

Question

[sabaghianamir70]

is there any such data ? and if it is, how can i download it . i need it for extract ribosomal rna from RNA seq data .

[ATpoint]

Download Rrna Sequences

sabaghianamir70, please use the search function for these kind of questions. You seem to get started with NGS analysis now so it is normal and expected that you'll have many questions as we all had when we got started. Still, most (if not all) standard questions that come up during analysis have been asked multiple times before both here and in other communities (e.g. SeqAnswers, SE Bioinformatics, Reddit, Bioconductor). Please use google and the search function thoroughly before opening posts (no offense intended) :)

[ATpoint]

Just that you know, it is the job of a moderator to make sure a community stays tidy and organized, that is why we encourage users to search first and then post, not vice versa. Otherwise we will have a dozen threads towards the same topic and information being spread across these, only making it more complicated to find good and definite answers.

[Madelaine Gogol]

Yep, I have used ensembl biomart for this, as linked in the first comment.

[sabaghianamir70]

as you can see in image i send, i done what VIPIN said, but this comes up and said the sequences are unavalibale, whould you tell me what part i did wrong.

[GenoMax]

Under sequence attribute you have peptide sequence selected (which is the default). Change that to cDNA sequence and you will get the sequences. Looks like there are 74 genes annotated as rRNA.

[sabaghianamir70]

but how i should use this as refrence , i want to detect rRNAs from my raw data. i think it ist what i need ??

[GenoMax]

You can create an index (with aligner of your choice) and then align your reads against that index. I suggest you use the human rDNA repeat I posted a link for below since it is a single contiguous sequence.

[sabaghianamir70]

im using galaxy and i dont know how can put these short rRNAs sequences put together as reference for my analyze. what i looking for is to extract rRNA contamination from my data, but every where i looked, didnt understand what should i exactly do .

[GenoMax]

1. Download the sequences from BioMart as a multi-fasta file.
2. Upload them to galaxy.
3. Choose that file as "reference genome" when you create an index with aligner you want to use.
4. Align reads against this reference.
5. Collect reads that don't map. That set would be your cleaned reads.

[sabaghianamir70]

thank you my friend <3

Answer 1

[GenoMax]

Sequence of human rDNA repeat: http://www.ncbi.nlm.nih.gov/nuccore/U13369

There are 400 copies of this unit on 5 chromosomes (http://nar.oxfordjournals.org/content/early/2011/02/25/nar.gkq1326.full )

Edit: Latest paper https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207531

Answer 2

[tomas4482]

Concatenate the following two fasta into one. Then make index with Bowtie.

5S rRNA

https://www.ncbi.nlm.nih.gov/nuccore/23898

47S rRNA

https://www.ncbi.nlm.nih.gov/nuccore/U13369.1