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