Mate pair bam files

Question

[fatima.shihab]

I need to download a sample BAM file which includes paired end reads. Can anyone help me with where to find online sample files for so?

Thank you in advance

Answer 1

[mastal511]

Try NCBI's SRA or the ENA.

[fatima.shihab]

could you provide me with a link?

[rlapoint11]

You can find SRA runs with aligned data and "mate pair" somewhere in the description using Entrez: http://www.ncbi.nlm.nih.gov/sra?term=%28aligned%20data[Properties]%29%20AND%20mate%20pair[Text%20Word]

You'll need to use the SRA's sam-dump with samtools to convert the SRA run to a bam file $ sam-dump SRR2149876 | samtools view -bS - > SRR2149876.bam

[mastal511]

But note that, although the two reads of a read pair may be described as 'mates', 'mate pair' reads are not the same thing as paired end reads, so searching for 'mate pair' may not give the desired result if what you are looking for is paired end reads..