Extraction of aligned read using samtools
Hi, I have aligned paired end RNA-Seq data and have the BAM file. I want to get the aligned reads using samtools. My command is : samtools view -b -F 4 filename.bam > mapped_out.bam Is it right for the paired end data? Also, when I am using the command, the generated file is found to be bigger than the input file. I would be grateful if anyone can help me to understand this.
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I think this answer can help you figure out how to do the job. how to extract pair end reads from bam file using samtool
Please use the search function, this question has been asked very often before. File size is not a good measure for anything. Count reads with
samtools flagstatinstead as file size depends on data composition and compression level.