Dear all,
we noticed some inconsistencies in the read lengths of the GEM
mappings (I didn't check the BWA mappings, but it's probably the
same).
Some samples appear to have up to 76 bp matched, while other samples
only have 75 bp. In regard to comparability this might cause some
(probably very little) differences between the samples.
i.e.
NA20589.1.M_111124_3.bam has 75 bp
NA20812.2.M_111216_6.bam has 76 bp
NA20760.3.M_120202_5.bam has 75 bp
NA20783.4.M_120208_6.bam has 75 bp
NA20768.5.M_120131_1.bam has 75 bp
NA20798.6.M_120119_6.bam has 75 bp
NA20803.7.M_120219_1.bam has 75 bp
We checked some more files for institute 2, and they seem to have
generally 1 bp more than the others.
We're also a bit lost regarding GEM's quality score. We would like
to filter reads for good mapping quality, we're just not sure how to
accomplish this.
Below are two read pairs as an example.
The fist pair has a mapping quality of 180. The second read however
was terribly aligned.
The second pair has only a quality of 99, while the reads mapped
much better (at least I would say so).
We're not sure what's the reason for this.
Curiously, both reads of a pair get the same mapping quality. This
could be by intention (i.e. it's always the pair quality rather than
the read quality) or, which could also explain the quality
differences for the reads, both reads of the pair get the quality of
the first mapped read.
We're thankful for any suggestions on how to filter for 'good'
mappings.
HWI-ST661:153:D0FTJACXX:8:2201:16410:93092
163 chr1 14704 180 75M = 14770
-134
CCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGGCTGACACGCGGG
CCCFFFFFHHHGHJJJIGIJIIIIIJIJHIIJJJB?BFHG7@F@AB:9=(6=(;>B29<@###############
RG:Z:0 NM:i:7 XT:A:U md:Z:62T12
XA:Z:chr15,-102516387,75M,8;chr9,+14815,75M,10;chr16,+64389,19M1I1M2I52M,10;chr2,-114356235,75M,11;
HWI-ST661:153:D0FTJACXX:8:2201:16410:93092 83 chr1
14770 180 39M1D22M1I3M2I1M1I2M4S = 14704
134
ACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCAGGTCCTTTCCCAGAGATGCCTTGGCTCGTGGCTGT
5@
9DDDDDDDDDC@BDDDDDDFHHIIIIJIHFJJJJIIJIJIJJIJJJJJJJJJJIIIJJJJHHHHHFFDDA11B
RG:Z:0 NM:i:7 XT:A:U
md:Z:(4)2>1-1>2-T2>1-22>1+39
XA:Z:chr15,+102516328,1S1M2I4M3I1M1I1M1I24M1D36M,8;chr9,-14881,39M1D22M1I3M2
I1M1I2M4S,10;chr16,-64452,39M1D22M1I3M2I1M1I2M4S,10;chr2,+114356176,1S1M2I4M3I1M1I1M1I24M1D36M,11;
HWI-ST661:153:D0FTJACXX:8:2201:6270:52066
99 chr1 14582 99 1M2I71M1S =
14665 158
CCCTGGTTCCGTCACCCCCTCCCAGGGAAGCAGGTCTGAGCAGCTTGTCCTGGCTGTGTCAATGTCAGAGCAACA
@11ADFFFHHHHHIIJJJJIJJIJJJJHHJJIJJHIJJJIIGFGIIJIIJF@@EGDAE>?)).7?BDFFDCCCB@
RG:Z:0 NM:i:8 XT:A:U md:Z:1>2-21A5T29C13(1)
XA:Z:chrY,-59358087,75M,4;chrX,-155255081,75M,4;chr9,+14691,75M,7;chr2,-114356359,75M,7;chr16,+64266,75M,8;chr12,-90971,75M,8;
HWI-ST661:153:D0FTJACXX:8:2201:6270:52066 147 chr1
14665 99 75M = 14582 -158
GGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTAGGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGTG
<B@A<9;>@CAAADDDDCCC>CC=?;>FHCGGEGIGJJIIGGIHHIIIIJIIJIJIGJJIJIHHFDDFFFFDB@;
RG:Z:0 NM:i:8 XT:A:U md:Z:AG38G34
XA:Z:chrY,+59358002,75M,4;chrX,+155254996,75M,4;chr9,-14776,75M,7;chr2,+114356274,75M,7;chr16,-64350,58M1I1M2I11M1D2M,8;chr12,+90885,2M1D73M,8;
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)