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Old 12-12-2013, 11:38 PM   #1
momo
Junior Member
 
Location: china

Join Date: Jul 2011
Posts: 1
Question HELP!! XS tag to filter unique reads Do NOT match bowtie2 report

I find the XS tag filtering the uniquely mapped reads number is different from the bowtie2 report. I first extract the flag number of 147/99 + 163/83 and it matches the reported 'aligned concordantly exactly 1 time' + 'aligned concordantly >1 times'. But when I extract the pairs with both reads tagged XS and find the number is a bit larger than the reported 'aligned concordantly >1 times'. I wonder what reads bowtie2 reported as unique...

Here is the output of bowtie2:
28115453 reads; of these:
28115453 (100.00%) were paired; of these:
9177458 (32.64%) aligned concordantly 0 times
15185809 (54.01%) aligned concordantly exactly 1 time
3752186 (13.35%) aligned concordantly >1 times
----
9177458 pairs aligned concordantly 0 times; of these:
2358270 (25.70%) aligned discordantly 1 time
----
6819188 pairs aligned 0 times concordantly or discordantly; of these:
13638376 mates make up the pairs; of these:
9978644 (73.17%) aligned 0 times
1757628 (12.89%) aligned exactly 1 time
1902104 (13.95%) aligned >1 times
82.25% overall alignment rate

and the numbers I get:
flag:
147/99 9471127
163/83 9466868

Pairs with XS tag
0 read get XS tag:13757424
1 read get XS tag:1358209
2 reads get XS tag:3822362
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