How Can I Download Data That Corresponds Only To A Specific Chromosome

Question

[Mary]

Hi all

I have downloaded some reads but when I align them against chromosome 10, only 4% of my reads will be aligned. but I want to have some reads which mostly belongs to one specific chromosome like Chr10. Where I can download these kind of data?

Thanks for any advice on this

[Istvan Albert]

typically you cannot download data to just one specific chromosome - as shown below your best option is to extract from the data subsets that match some condition

Answer 1

[Sukhi Singh]

Which data you downloaded. I would recommend to go to NCBI GEO, which is a public genomics data repository. Search for a bam file (which is a mapped file) and then you can extract information from it, using

samtools view file.bam | egrep -w 'chr10' > readMappingtoCHR10.

Samtools need to be installed for that or if you have a sam file (human readable), just use

egrep -w 'chr10' file.sam > readMappingtoCHR10

You can use this bamfile from this page, for your test.

Before mapping you wont be able to know, if the reads are mapping to chr10 or somewhere else unless you know the biological background of data (eg protein binding to only chr10 genes etc.)

[Mary]

Finally I want to create Haplotype from my aligned reads.but there is only 66123 aligned against chromosome 10.(only 4% of whole reads)Is these reads enough to make Haplotype or what..? thanks

[Istvan Albert]

if you have a new question please post it separately - appending it to a answer of a different question is not a good way to get answers

Answer 2

[Laura]

The 1000 genomes data set contains lots of bam files and combined with samtools view you should be able to get data aligned to just one chromosome

Our bam files are found in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data

An instructions on how to get subsections can be seen here

http://www.1000genomes.org/faq/how-do-i-get-sub-section-bam-file