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Hi, all
I'm new to process Solid data (75+35 PE). I used Botie to alingn them. After successfully getting the SAM results, I found that for paried-end aligned reads, the insert length information are weird. The insert length in one pair (mapped to plus strand) are always shorter 2 bp than that of its pair in minus strand. I pasted some lines as following. I think they should be same. I also tried BWA and the insert length information are correct. Any ideas? Thanks.
1_31_346_F3 99 chr13 99114985 255 73M = 99115091 139
1_31_346_F5-DNA 147 chr13 99115092 255 33M = 99114984 -141
1_31_579_F3 99 chr15 51708168 255 73M = 51708301 166
1_31_579_F5-DNA 147 chr15 51708302 255 33M = 51708167 -168
I'm new to process Solid data (75+35 PE). I used Botie to alingn them. After successfully getting the SAM results, I found that for paried-end aligned reads, the insert length information are weird. The insert length in one pair (mapped to plus strand) are always shorter 2 bp than that of its pair in minus strand. I pasted some lines as following. I think they should be same. I also tried BWA and the insert length information are correct. Any ideas? Thanks.
1_31_346_F3 99 chr13 99114985 255 73M = 99115091 139
1_31_346_F5-DNA 147 chr13 99115092 255 33M = 99114984 -141
1_31_579_F3 99 chr15 51708168 255 73M = 51708301 166
1_31_579_F5-DNA 147 chr15 51708302 255 33M = 51708167 -168