samtools + map
I did a mapping in bowtie2 using paired-end reads. Suppose I have R1 and R2. When R1 and R2 I have a mapped properly paired, correct? I can to identify which of the R (R1 or R2) were mapped?
Thank you very much.
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elfeusilva •
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If you want singletons then samtools view -F 4 -f 8 foo.bam will print them out. The flags indicate that the current read is mapped but its mate isn't. To identify which of the reads this is, look at the 0x40 and 0x80 bits. If you wanted, you could combine those with the aforementioned command to get only singletons from read #1 or #2.
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It is really hard to understand what exactly you are trying to ask. Kindly rewrite your question.
I would like to make a subset with only singletons reads. What parameter I use in samtools to retrieve only the singletons?
singletons: uniquely mapped reads?