Hello!
I am currently working with a dataset of Illumina PE reads (length 100bp, fragment 500bp). Now, I know the definition for Bowtie's YT tag and the various values "CP", "UU", "UP", "DP", but I have stumbled upon an example where I do not understand why the pair has been assigned the YT:Z:UP tag.
Here are the pairs alignment:
FCC0WRYACXX:4:1115:3531:40304#ATGAGGAA 113 Chr6 3218530 12 100M Chr2 3121587 0 ATATCGCA...AGCTATCA qual AS:i:-5 XS:i:-17 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:9T90 YT:Z:UP
FCC0WRYACXX:4:1115:3531:40304#ATGAGGAA 177 Chr2 3121587 0 100M Chr6 3218530 0 ACTACTAG...ATCGATAG qual AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP
I would expect these to be considered discordantly mapped (DP) and not UP. Admittedly one of them has a MAPQ of 0, but it is mapped. Should have an '*' in some fields if it was not mapped (and then I would understand the UP.
Any ideas how to explain this behaviour?
I tried finding the similar problem mentioned in other threads but couldn't find quite the same situation.
Cheers
I am currently working with a dataset of Illumina PE reads (length 100bp, fragment 500bp). Now, I know the definition for Bowtie's YT tag and the various values "CP", "UU", "UP", "DP", but I have stumbled upon an example where I do not understand why the pair has been assigned the YT:Z:UP tag.
Here are the pairs alignment:
FCC0WRYACXX:4:1115:3531:40304#ATGAGGAA 113 Chr6 3218530 12 100M Chr2 3121587 0 ATATCGCA...AGCTATCA qual AS:i:-5 XS:i:-17 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:9T90 YT:Z:UP
FCC0WRYACXX:4:1115:3531:40304#ATGAGGAA 177 Chr2 3121587 0 100M Chr6 3218530 0 ACTACTAG...ATCGATAG qual AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP
I would expect these to be considered discordantly mapped (DP) and not UP. Admittedly one of them has a MAPQ of 0, but it is mapped. Should have an '*' in some fields if it was not mapped (and then I would understand the UP.
Any ideas how to explain this behaviour?
I tried finding the similar problem mentioned in other threads but couldn't find quite the same situation.
Cheers
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