Filter SAM file for read pairs that align on same strand

I want to filter a SAM file for read pairs that align to the same strand. That is for R1 and R2, I want the alignment to be either both on the forward strand (FF) or both on the reverse strand (RR).

I used samtools view -F 0x2 to exclude any instance where the pairs align correctly (FR) but it looks like it's still including some FR reads with short read 1 lengths.

How can I filter a SAM file to only give me read pairs that align on the same strand, either both reads on the forward strand or both reads on the reverse strand?

samtools alignment sam

• 796 views • link

updated 1.5 years ago by Pierre Lindenbaum

• written 1.5 years ago by kmyers2 •

1 answer

samtools view -e 'flag.paired && !flag.unmap && !flag.munmap && ((flag.reverse && flag.mreverse) || (!flag.reverse && !flag.mreverse))' in.bam

• 0 views • link

written 1.5 years ago by Pierre Lindenbaum

More posts like this

bwa mem skip orientation when aligning a small subset of reads
written 3.1 years ago by Yihang •

For pair-end read files, `read1.fastq`, `read2.fastq`, I use the following command `cat read1.fastq | head -n 4000 > read1_first1000.fastq` (and `cat read2.fastq | head -n …
Looking for RNA-seq aligner that can identify not properly mapped paired
written 3.5 years ago by romain.lannes

Hi I would like to identify pairs in RNA seq that dot not map properly. In particular, I am interested on this kind of pattern: …
BWA-MEM : skip orientation FR as there are not enough pairs ?
written 3.6 years ago by Saran •

Hello, I have Paired End Data that I am trying to align to a very short reference(222 bp); I expect that the paired-end data have …
BWA mem skip orientation
written 7.3 years ago by williamsbrian5064

Hi, So I am not entirely sure if this is an issue or not. So to give a little background, I used bwa, picard, samtools, …
Orientation of reads in .fastq files from RNA-Seq
written 7.8 years ago by newbio17

I have R1.fastq and R2.fastq from RNA-Seq experiment. I'm currently trying to perform differential expression using Salmon and DESeq2. Since the RNA-Seq was done using …
R1 and R2 matching
written 7.9 years ago by ieie •

Dear all, I have a number of X_R1_001.fastq.gz X_R2_001.fastq.gz and I would to match them. I have seen a pipeline where they give this: # …
Strand specific pair end sequencing
written 9.4 years ago by Bioinfonext

I have a strand-specific pair-end Illumina sequencing data. I am not able to understand which option to use in the different software. For each library …
R1 and R2 in sequencing data
written 9.8 years ago by blur

Hi, I find myself a little confused about the diractionalityof R1 and R2 reads. The R2 is always the opposite direction of R1, but R1 …
bowtie --fr/--rf/--ff reporting
written 10.0 years ago by ThePresident

Hello, I am mapping Illumina generated paired-end reads with bowtie. By default, bowtie reports --fr, i.e. paired mates are in Forward/Reverse position (which is normally …
How to align Trimmomatic unpaired reads with BWA?
written 11.3 years ago by mcff23 •

Hi everyone! I have filtered the adapters from my Illumina PE reads with *Trimmomatic*. This was the output (as I expected): ``` sample.R1.trimmed.fastq sample.R2.trimmed.fastq sample.R1.unpaired.fastq …