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Old 09-14-2017, 05:51 AM   #1
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Location: Adelaide

Join Date: Sep 2017
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Default Samtools how many reads were mapped as a pair

Hey, I am new to bioinformatics. I get stuck on the question How many reads were mapped as a pair.
I have created a .bam file that only contains mapped reads. Then, I need to figure out three questions.
How many reads were mapped?
How many reads were mapped as a pair?
How many reads were mapped as a "proper" pair?
I can solve the 1st and 3rd question, but I am confusing about the 2nd question. After searching on google, I have found the following code:
samtools view -F 0x40 filename.bam | cut -f1 | sort | uniq | wc -l
samtools view -f 0x40 -F 0x4 filename.bam | cut -f1 | sort | uniq | wc -l #left mate
samtools view -f 0x80 -F 0x4 filename.bam | cut -f1 | sort | uniq | wc -l #right mate
source from :
I don't sure it works or not. Can anyone help me?

Also, I need to find the Arabidopsis thaliana gene that associated to AT3G13276 and identify how many inserts mapped to that region. Does this need to use IGV to solve it?
Fay.huo is offline   Reply With Quote

bioinformatics question, igv, samtools

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