Extraction of aligned read using samtools
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5.3 years ago
Neu ▴ 10

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.

RNA-Seq sequencing next-gen • 991 views
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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

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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 flagstat instead as file size depends on data composition and compression level.

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