BAM record error: found spliced alignment without XS attribute

paolo.kunder

Member

Join Date: Aug 2011
Posts: 93

BAM record error: found spliced alignment without XS attribute

09-06-2012, 06:09 AM

Dear All,
I have browsed old forums but I really don't know how to fix problem,
I mapped SOLiD reads with LifeScope, then I run both cufflinks and cuffmerge, now when I run cuffdiff I encounter the XS tag problem, how do i fix it?
any experience?

from cufflinks web site:

However Cufflinks will accept SAM alignments generated by any read mapper. Here's an example of an alignment Cufflinks will accept:
and what about cuffdiff?

thanks,
paolo

samfile:

Code:

691_1862_244    16      chr1    3000885 1       5S25M20S        *       0       0       CTGCGGGCATTNNGTACCATGCGGNNNGGGTAATAACGGAAATAATTGTA      ...367...-+%(
CFFJJJJJJ?3*#'+,,52222222221111112444   RG:Z:SHAM_1     NH:i:1  CM:i:2  NM:i:0  CQ:Z:/?;//@@@//;@;6666@@/?>6/22//2@@2/<2@@/26@@?@=@62@@ CS:Z:T031103033002031
03303100010003313101310110313003312
426_2037_1220   16      chr1    3034383 1       5S25M3S17H      *       0       0       GACAGTCTTTTAAGCCCGTGGTTGTGTCTNCGN       //4559:::9088GAJJJJJJJJJJHFF2
)1+'    RG:Z:SHAM_1     NH:i:1  CM:i:2  NM:i:3  CQ:Z:/@@@22@/88/@<8@/@//2@//@2/6/@=6@/6>6>/@;/@;@28@=2< CS:Z:T32223212221022230133202211110101130032030002212
112
670_1721_1819   0       chr1    3063656 5       20S27M3S        *       0       0       CCCCCCACTTTGAGGGTTTCACAAACAGAGGCATAAGGNNNNAGTGTCNN      >644444444444
6888<AE>>DJJJJJJJJJJJJ:90$&$&+577?-*)   RG:Z:SHAM_1     NH:i:1  CM:i:2  NM:i:0  CQ:Z:6//@=6@/@=6?@/2@@26;@@//6=@/@@@2@8?/@/*/</2.2@@//2 CS:Z:T200000112001220
01002111001122203133020200232111200

Last edited by paolo.kunder; 09-06-2012, 06:13 AM.

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BAM record error: found spliced alignment without XS attribute

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