Question: samtools + map
0
gravatar for elfeusilva
5.6 years ago by
elfeusilva0
Afghanistan
elfeusilva0 wrote:

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.

ADD COMMENTlink modified 5.6 years ago by Devon Ryan93k • written 5.6 years ago by elfeusilva0

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

ADD REPLYlink written 5.6 years ago by Ashutosh Pandey11k

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

ADD REPLYlink written 5.6 years ago by elfeusilva0

singletons : uniquely mapped reads ? 

ADD REPLYlink written 5.6 years ago by Nicolas Rosewick8.5k
1
gravatar for Devon Ryan
5.6 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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.

ADD COMMENTlink written 5.6 years ago by Devon Ryan93k
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