Question: first and second mate reports by samtools 0x40 and 0x60 FLAGs
0
gravatar for R
4.2 years ago by
R10
....
R10 wrote:

Hi I would like to separate 1/2 mates of a paired-end bam file.

To see first mate:

samtools view -F 0x40 in.bam

To see second mate:

samtools view -F 0x80 in.bam

but it returns the following as first mate (0x40):

H0544AFXX:1:11101:8739:1038 163 chr3 17908775 3 1S74M = 17909029 330 ...

and for example this one as second (0x80):

NS500173:56:H0544AFXX:1:11101:8739:1038 83 chr3 17909029 3 75M = 17908775 -330

while Flag 163 means:

    read paired
    read mapped in proper pair
    mate reverse strand
    second in pair

and 83:

    read paired
    read mapped in proper pair
    read reverse strand
    first in pair

It would be great if somebody could clarify this issue. thanks

sequencing rna-seq alignment • 1.6k views
ADD COMMENTlink modified 4.2 years ago by pengchy410 • written 4.2 years ago by R10
1
gravatar for pengchy
4.2 years ago by
pengchy410
China/Beijing
pengchy410 wrote:

From the definition of the parameter, "-F" will filter the reads with the flag, while "-f" will give your required flag. So you have misunderstand the parameters.

         -f INT   required flag, 0 for unset [0]
         -F INT   filtering flag, 0 for unset [0]

ADD COMMENTlink written 4.2 years ago by pengchy410
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