Question

samtools + map

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10.0 years ago

elfeusilva • 0

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.

properly-paired samtools bowtie singletons • 2.6k views

ADD COMMENT • link updated 2.6 years ago by Ram 43k • written 10.0 years ago by elfeusilva • 0

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It is really hard to understand what exactly you are trying to ask. Kindly rewrite your question.

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 10.0 years ago by Ashutosh Pandey 12k

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I would like to make a subset with only singletons reads. What parameter I use in samtools to retrieve only the singletons?

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 10.0 years ago by elfeusilva • 0

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singletons: uniquely mapped reads?

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 10.0 years ago by Nicolas Rosewick 10k

score 2 · Answer 1 · 2014-04-30

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.