I'm forwarding this to Paolo, I'm not sure if he's on the geuvadis
analysis group list - I think he's the right person to answer
these questions.
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen@unige.ch
On 7/4/12 4:28 PM, Matthias Barann wrote:
Hi,
we were expecting that both reads of a pair would have different
quality scores. Maybe the data below makes our problem a bit more
clear.
The majority of pairs have the same quality value for both reads
(see below), despite a large difference in the CIGAR string. It is
not clear to us, why reads with a cigar string like:
1S1M2I3M1I4M1D2M1D60M1S have the same quality as a perfect
match. We would have expected that non-perfect matches have a
lesser mapping quality.
- Matches which are unique, and do not have any subdominant
match:
251 >= MAPQ >= 255, XT=U
- Matches which are unique, and have subdominant matches but
a different score:
175 >= MAPQ >= 181, XT=U
- Matches which are putatively unique (not unique, but
distinguishable by score):
119 >= MAPQ >= 127, XT=U
- Matches which are a perfect tie:
78 >= MAPQ >= 90, XT=R.
If I understand this correctly, the cigar string does not
contribute to the mapping score? That would explain it then,
though I must admit I feel a bit uncomfortable with reads that
were mapped uniquely by splitting them in 10 parts or more (score
>= 180).
How do you take care of this? Do you clip the reads manually?
HWI-ST661:153:D0FTJACXX:7:1101:1261:74388
99 chr11 63764389 180 25M108N50M
HWI-ST661:153:D0FTJACXX:7:1101:1261:74388 147
chr11 63764583 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:98650 99 chr4
88128614 255 1S73M1S
HWI-ST661:153:D0FTJACXX:7:1101:1261:98650 147 chr4
88128727 255 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:102235 99
chr5 21883611 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:102235 147
chr5 21883892 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:123302 163 chr5
134262601 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:123302 83 chr5
134262672 180 1S74M
HWI-ST661:153:D0FTJACXX:7:1101:1261:154720 163
chr6 32827449 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:154720 83
chr6 32827520 180 1S43M3D31M
HWI-ST661:153:D0FTJACXX:7:1101:1261:174904 99 chr17
46973042 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:174904 147 chr17
46973131 180 2S15M1D58M
HWI-ST661:153:D0FTJACXX:7:1101:1261:188083 163
chr22 22764112 255 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:188083 83
chr22 22764366 255 75M
HWI-ST661:153:D0FTJACXX:7:1101:1261:188990 163 chr7
127361327 180 1S1M2I3M1I4M1D2M1D60M1S
HWI-ST661:153:D0FTJACXX:7:1101:1261:188990 83 chr7
127361431 180 24M86083N51M
HWI-ST661:153:D0FTJACXX:7:1101:1262:7502 99
chr17 40024125 180 33M804N42M
HWI-ST661:153:D0FTJACXX:7:1101:1262:7502 147
chr17 40025749 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:22026 99 chr6
32611046 180 74M1S
HWI-ST661:153:D0FTJACXX:7:1101:1262:22026 147 chr6
32611141 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:72904 163
chr16 33962893 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:72904 83
chr16 33963059 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:120662 99 chr2
107314958 119 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:120662 147 chr2
107315099 119 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:122435 145
chr1 91852782 180 55M
HWI-ST661:153:D0FTJACXX:7:1101:1262:122435 97
chr12 127650913 255 16M1D58M1S
HWI-ST661:153:D0FTJACXX:7:1101:1262:126215 163 chr10
13375888 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:126215 83 chr10
13380697 180 2S73M
HWI-ST661:153:D0FTJACXX:7:1101:1262:136701 163
chr14 50085541 255 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:136701 83
chr14 50085669 255 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:180551 99 chr5
88047745 180 75M
HWI-ST661:153:D0FTJACXX:7:1101:1262:180551 147 chr5
88057001 180 2M1I3M2I47M
best wishes,
Matthias & Daniela
--
Matthias Barann
Institute of Clinical Molecular Biology
Christian Albrechts University Kiel
Schittenhelmstr. 12
D-24105 Kiel, Germany
m.barann@ikmb.uni-kiel.de
+49 - (0)431 - 597 8681 (office)
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