Hi lishiyong,

Most likely your refGene_hg18.gtf file is not sorted correctly. You have to sort by chr and then by start coordinate.

Anney ________________________________________ From: lishiyong [lishiyong@genomics.org.cn] Sent: Thursday, March 31, 2011 3:39 AM To: galaxy-user Subject: [galaxy-user] cufflinks FPKM

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

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 lishiyong@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

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lishiyong

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