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  • 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
    

      

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  • 原文地址:https://www.cnblogs.com/leezx/p/8655086.html
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