Question: Check if BAM is derived from pair-end or single-end reads?
3
gravatar for medranom38
2.4 years ago by
medranom3830
Cambridge, MA, USA
medranom3830 wrote:

I'm automating a pipeline and currently a user inputs as a parameter if the input BAM is from pair-end or single-end reads. I want to automatically check this. How can do I this?

single-end pair-end bam • 6.0k views
ADD COMMENTlink modified 4 weeks ago by Hakubi0 • written 2.4 years ago by medranom3830

Thanks to Pierre's suggestion, I also got to understand this issue. Following link http://www.htslib.org/doc/samtools.html provides additional useful information, especially mentioned about flags. If in.bam is made of totally single end reads, following command probably returns 0. The option '-f 1' can be substituted for '-f 0x1' in hexadecimal.

samtools view -c -f 1 in.bam
ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Hakubi0

Hello Hakubi and welcome to biostars,

your post is better placed as a comment. To do this please use the ADD COMMENT button below the post you like to reply to. Answers should only be used to respond to the original question at the top of this page and should answer the question as best as possible. Links to pages that contain further information are always welcome as a comment.

So I moved your post to a comment. As you can see this is not perfect, as your reply would be better match as a comment on Pierres answer.

Happy writing.

fin swimmer

ADD REPLYlink written 4 weeks ago by finswimmer3.6k

Hello fin swimmer

Thank you for correcting my mistake. I make sense of good manners.

Hakubi

ADD REPLYlink written 4 weeks ago by Hakubi0
12
gravatar for Pierre Lindenbaum
2.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum110k wrote:

use the sam flag and 'samtools view -c -f 1 in.bam ' to test if your bam contains paired reads. ( 1= "read paired" http://broadinstitute.github.io/picard/explain-flags.html )

ADD COMMENTlink written 2.4 years ago by Pierre Lindenbaum110k
3
gravatar for ATpoint
2.1 years ago by
ATpoint5.7k
Germany
ATpoint5.7k wrote:

You may also use samtools view -H. It will print you the header of the bam, including the command that was used for the alignment. Usually, paired-end data are separated into two fastq files, one for forward/reverse reads. Hence, if the alignment command shows two fastq files to be used, it was a paired-end alignment.

An example where BWA mem was used:

samtools view -H my.bam

@PG ID:bwa PN:bwa VN:0.7.12-r1044 CL:/opt/bwa-0.7.12/bwa mem -M -t 24 /Genomes/hg19/hg19.fasta in_1.fastq in_2.fastq

where the general BWA mem paired-end command is (similar in Bowtie etc.):

./bwa mem -M -t threads indexedRefGenome.fasta in_1.fastq in_2.fastq > out.sam

ADD COMMENTlink written 2.1 years ago by ATpoint5.7k
1
gravatar for John
2.1 years ago by
John12k
Germany
John12k wrote:

Both methods suggested by Pierre and Alexander will work great for 99.99% of cases, but things get a little messy if you want to detect single-end-reads in a mixed paired & single BAM file, or singletons in a previously paired-end BAM file.

Detecting singles in a mixed file is easy, just look for 'samtools view -c -F 1 in.bam'

Detecting singletons is a bit trickier though... since the filtering step might have just removed the read and left the mate totally unaffected. Perhaps you could use the read names (although people have a habit of putting junk like /1 and /2 on the end of the read names) Or maybe one of Pierre's tools can detect orphaned singletons :)

Alexander's method would solve this very quickly and easily if all BAM files coming in are totally under your pipeline's control (you mapped/filtered them yourself at some point). But external "mystery BAMs" may have issues.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by John12k
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