Where can I download some example BAM files?

Question

[Federico Giorgi]

Hi all,

I am looking for an online repository for BAM files for teaching and testing purposes. It doesn't matter the genome they are mapped onto, but ideally they should be no bigger than 100MB. ENA (the European Nucleotide Archive) has some projects containing BAM files, but I cannot find them since this is not a queriable feature (the standard raw file is obviously FASTQ).

Can you help me? I promise you will be credited in all my lessons forever!

PS I know this post is a bit of a repetition of a previous one from 2014 (link), but the links shown there are either expired or contain files that cannot be downloaded (try it).

[seidel]

Could you request just a single chromosome of BAM files from 1000 Genomes? https://www.internationalgenome.org/faq/how-do-i-get-a-genomic-region-sub-section-of-your-files/

And these tutorials have yeast BAM files:

1. https://bioconductor.org/packages/devel/data/experiment/manuals/leeBamViews/man/leeBamViews.pdf
2. https://mimodd.readthedocs.io/en/latest/tutorial_example2.html

Answer 1

[JC]

In the 1000 Genomes there are plenty of BAM file, check the http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ location you can subselect alignments to chr11, chr22, or exomes.