BAM file download for just a few genes

Question

[Zahra]

Hi all,

I want to download the BAM file just for few genes and because Don’t need the whole data of patients, I can download it by my interest gene position. I tried to find my gene position in the UCSC and RefSeq, but they showed me different positions -very small difference- (I set my Reference genome on hg19 in both sites). Now I don’t know which one should I choose for download?

Could I randomly download 200bp upstream and downstream of my gene position? Does anyone have the same experience?

[ATpoint]

That is most likely going to mess up your analysis. The reads in an RNA-seq experiment are not independent of each other. It is the composition of the entire library that determines the distribution of reads across all genes. Generally you always want to download the entire file, analyze it as a whole, and then later filter the results for genes of interest. I strongly suggest to stick to that advise (and standard workflows) unless you have a good idea what you're doing.

[Zahra]

Thank you for your kind suggestion.

Answer 1

[Jorge Amigo]

samtools view is capable of pointing to a remote file and download only reads of interest. I used in the past to retrieve mitochondrial reads from 1000g bams instead of downloading the whole bunch of bam files available and extracting them locally, and it worked flawlessly:

samtools view -b http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam MT > HG00096.mt.bam