the refrence GTF file from Ensembl should have chr in the colum specifying Chrromosome number. Vasu
--- On Thu, 3/31/11, Paul Korir polariseke@gmail.com wrote:
From: Paul Korir polariseke@gmail.com Subject: Re: [galaxy-user] cufflinks FPKM To: "lishiyong" lishiyong@genomics.org.cn Cc: "galaxy-user" galaxy-user@lists.bx.psu.edu Date: Thursday, March 31, 2011, 8:39 AM
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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