Cufflinks requires an 'xs' tag on each read in the bam file. Only tophat does 
this. You can write a script to add this or remap with tophat. 

How much of a difference do you see between tophat and bioscope?

Please excuse any typos -- Sent from my iPhone

On Apr 11, 2011, at 9:46 AM, lishiyong <lishiy...@genomics.org.cn> wrote:

> 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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