怎么从bam文件中提取出比对OR没比对上的paired reads | bamToFastq | STAR

折腾这么多都是白瞎，STAR就有输出没有别对上的pair-end reads的功能

参见：How To Filter Mapped Reads With Samtools

I had the same issue but with Paired End Reads, and I solved using samtools and bamToFastq. You can find bamToFastq here: https://code.google.com/p/hydra-sv/ 

• If you need unmappedR1.fastq (containing both paired and unpaired R1 unmapped reads) and unmappedR2.fastq ( containing both paired and unpaired R2 unmapped reads). 

           Use samtools -f 4 to extract all unmapped reads :

samtools view -b -f 4 file.bam > file_unmapped.bam
bamToFastq -bam file_unmapped.bam -fq1 unmappedR1.fastq -fq2 unmappedR2.fastq

　　

• If you need unmappedpairedR1.fastq (containing only paired  R1 unmapped reads) and unmappedpairedR2.fastq ( containing only paired R2 unmapped reads). Meaning you need all paired reads where at least one of them is unmapped. 

           Use samtools -F 2 to discard only reads mapped in proper pair:

samtools view -b -F 2 file.bam > file_unmapped.bam 
bamToFastq -bam file_unmapped.bam -fq1 unmappedpairedR1.fastq -fq2 unmappedpairedR2.fastq