I am working with paired-end reads, and want to extract all those reads which map to an assembly. Since its a paired-end reads, I am confused if I should extract reads for which both (forward and reverse) end reads align to the assembly or extract reads for which at least one of the forward or reverse end reads maps. Which one should I go for and how? I know bowtie and samtools can be used for this purpose, but I don't know the specific options to choose for this purpose. Thanks!
You should use paired-end reads not the singleton reads. You can use following command from samtools to achieve it :
samtools view -f2 -o
If you want to understand the sam flags, here is the link : https://broadinstitute.github.io/picard/explain-flags.html
bedtools:
https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html
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