Question: Genomes on chromosome level
0
gravatar for Bara'a
5.1 years ago by
Bara'a250
Amman - Jordan
Bara'a250 wrote:

Hi all :)

Where can I find a credible and reliable source (website) for downloading genomes on chromosome level only ?!

I don't want contigs or scaffolds, or even cDNAs !!

Thanks in advance

assembly • 1.2k views
ADD COMMENTlink modified 5.1 years ago by Erik Wright380 • written 5.1 years ago by Bara'a250

Hi all :) I'm really sorry for what I'm about to do, but I have to cross-reference the same question on some other specialized forums since I have waited so long for the appropriate answer and no one seems willing to help , unfortunately :/ Greetings !!

ADD REPLYlink written 5.0 years ago by Bara'a250

Both my answer and Erik's answer are valid solutions for doing what you are trying to do. My guess is nobody suggested other options because ours are sufficient. You asked on a bioinformatics group and were given bioinformatics-based solutions. If you wanted an application that would download these for you, you should have explicitly said so.

ADD REPLYlink written 5.0 years ago by Brice Sarver3.6k

Thanks for the clarification, I truly appreciate your help and concern but I wrote earlier that I'm not familiar with R language and I don't want applications either ... just some kinda straightforward solution with the minimal confusion, I'm still a beginner in this field and need guidance !!

ADD REPLYlink written 5.0 years ago by Bara'a250
0
gravatar for Brice Sarver
5.1 years ago by
Brice Sarver3.6k
United States
Brice Sarver3.6k wrote:

Download any genome you want from any source, then subset that file based on the chromosome. Most are distributed as FASTA sequences. You could select among the chromosomes easily (and within a loop!) by using Biostrings in R, amongst a ton of other programming options.

library(Biostrings)
a <- readDNAStringSet("your_genome.fa", format="fasta")

#show the data structure
a

#the chromosome names are stored in
names(a)

#and you could write to a new file with:
b <- a[whatever chromosome you want]

writeXStringSet(b, file="your_chromosome.fa", format="fasta")
ADD COMMENTlink modified 13 months ago by Ram32k • written 5.1 years ago by Brice Sarver3.6k

This seems that should be done for each chromosome individually, isn't it ?!

I will try to do so, thanks a lot ^_^

ADD REPLYlink written 5.1 years ago by Bara'a250

You got it. Wrap it in a loop across indices/chromosome names.

ADD REPLYlink written 5.1 years ago by Brice Sarver3.6k
0
gravatar for Erik Wright
5.1 years ago by
Erik Wright380
Erik Wright380 wrote:

See the answer to this question:

A: All completed genomes for a phyla

ADD COMMENTlink modified 13 months ago by Ram32k • written 5.1 years ago by Erik Wright380

@Erik Wright ...

I took a look at the answers in that thread, and yours seems not applicable to me since I'm not familiar with R language.
Is there any other options to download the full genomes in chromosomes level ?!
I would be very grateful if you can help me out in this .

ADD REPLYlink written 5.0 years ago by Bara'a250
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