Hi,
I used dwgsim to create simulated read pairs.
Then, I aligned these read pairs to the reference genome with Bowtie2.
I obtained 5063956 reads pairs with insert size =0
5063956
What does it means?
IGV uses color coding to flag anomalous insert sizes. When I look these read pairs with insert size=0, it appear in grey. In IGV grey is for inserts that are like than expected.
This the flagstat result (file.bam):
10022022 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
9979404 + 0 mapped (99.57%:-nan%)
10022022 + 0 paired in sequencing
5011011 + 0 read1
5011011 + 0 read2
4958066 + 0 properly paired (49.47%:-nan%)
8789364 + 0 with itself and mate mapped
1190040 + 0 singletons (11.87%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
This is the results I obtain according to the insert size column (file.bam):
Mapped in correct orientation and within insert size (i.e properly paired) : 4958066
Mapped uniquely but wrong insert size : 3831298
Both unmapped : 38188
One of the mate is unmapped : 1194470
Mapped within the insert size but wrong orientation: 0
I notice that 3831298+38188+1194470=5063956, it correspond reads pairs with insert size =zero
Someone can help me?
I used dwgsim to create simulated read pairs.
Then, I aligned these read pairs to the reference genome with Bowtie2.
I obtained 5063956 reads pairs with insert size =0
Code:
samtools view file.bam | awk '{ if ( $9 ==0){print $0;} }' | wc -l
What does it means?
IGV uses color coding to flag anomalous insert sizes. When I look these read pairs with insert size=0, it appear in grey. In IGV grey is for inserts that are like than expected.
This the flagstat result (file.bam):
10022022 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
9979404 + 0 mapped (99.57%:-nan%)
10022022 + 0 paired in sequencing
5011011 + 0 read1
5011011 + 0 read2
4958066 + 0 properly paired (49.47%:-nan%)
8789364 + 0 with itself and mate mapped
1190040 + 0 singletons (11.87%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
This is the results I obtain according to the insert size column (file.bam):
Mapped in correct orientation and within insert size (i.e properly paired) : 4958066
Mapped uniquely but wrong insert size : 3831298
Both unmapped : 38188
One of the mate is unmapped : 1194470
Mapped within the insert size but wrong orientation: 0
I notice that 3831298+38188+1194470=5063956, it correspond reads pairs with insert size =zero
Someone can help me?
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