Hi Li,

I think the solution lies in changing the chromosome names in the GTF file
(refGene_hg18.gtf) from a number e.g. '1' to 'chr1'.

Paul

2011/3/31 lishiyong <lishiy...@genomics.org.cn>

>  Hi:
>
>
>        I gain the SOLiD sequencing data.I used bowtie to map human genome
> then I sort the sam file .I used cuffinks to calculate FPKM with the sam
> file ,human gtf file .it gives 0 FPKM values and this is for all genes
> .what's the reason?
>
> (1)
> bowtie -C human_hg18_color -f F3.csfasta -Q F3_QV.qual -v 2 -k 100 -p 6 
> --mapq  --sam test.sam
>
> (2)
> samtools view -uS test.sam  2>/dev/null  | samtools sort -m 2000000000 - 
> test.bam
>
> (3) cufflinks -G refGene_hg18.gtf test.bam.bam
> 2011-03-31
> ------------------------------
> lishiyong
>
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-- 
Paul Korir
www.paulkorir.com
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