Hi：
I use the solid PE sequencing data and mapped with the bioscope tools(AB
company supported) ，which is better for solid data mapping ,so I don't use the
bowtie to map . Ｉgain the BAM file! Now ,I want use the cufflinks to calculate
the gene expression. But there is a error.
[15:08:06] Inspecting reads and determining fragment length distribution.
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
the BAM file :
323_358_2010 73 chr1 343 0 45M5H * 0 0
CCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCT
IIIIIIIIIII))C/1<DE''@DAHD379AID1;7BI+'7))I?3 RG:Z:20110328192522421 NH:i:0
CM:i:4 SM:i:2 CQ:Z:A=ABA<<>@?<4)='))415'-4118-'1)9>'+1'<6+'1)85+)-+6-
CS:Z:T20023010023110230100030100230100230100030000200000
423_236_1955 81 chr1 550 0 8H42M = 699451 698945
GTGCAGAGGAGAACGCAGCTCCGCCCTCGCGGTGCTCTCCGG
GF>IIII%%III))8IIII?IIII%%IIIIIIIIIIIIIIII RG:Z:20110328192522421 NH:i:2
CM:i:5 SM:i:3 CQ:Z:9BA<AAB>;?AB:55;A%9?AB,4:@@*/)7>2<%5@<:3,;-.%8.*;5
CS:Z:T20302222311033322303302232133302223222131122330223
298_1884_1495 113 chr1 562 0 7H43M chr3 199392032
0 ACGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGG
5AI;6:>AIIII>?I7FIEIIIIIIIIIIIIIIIIIIIIIIII RG:Z:20110328192522421 NH:i:2
CM:i:0 SM:i:3 CQ:Z:BB@7<AB8@ABA=2;=>82:?A388.A&28(77;64.1*-/<&0:9/%3?
CS:Z:T20221231112210030222231103332200330223213312222022
62_1428_1954 89 chr1 562 1 50M * 0 0
ACGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGGAGAATGC
*=AIII4/CII=%%I((=EIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:20110328192522421
NH:i:0 CM:i:4 SM:i:0
CQ:Z:@B@BABB=ABBB?@A=B>>@@?<;?>B>=<??'7(;A%&849+%0:@.4*
CS:Z:T13130222022123111221003022223110331222033022321331
I have sorted the bam file and the gtf file.
cufflinks -G refGene_hg18.gtf -p 3 -r human_hg18.fa -o test test.pe.bam
(the version of cufflinks is v0.9.2 )
Who know the reason ,and what shoud I do!
best wishes!
Shiyong Li
2011-04-11
lishiyong
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