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Old 06-08-2010, 11:49 PM   #3
oliviera
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Location: germany

Join Date: Apr 2010
Posts: 31
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Dear sjm,

Thanx for your answer. I will try to do as you say. I am not sure of it, but I thought that providing the gff file to tophat will help the mapping of the reads, that s why I thought to provide the gff file in tophat. Is it indeed the case?

Here are the first lines I got with cufflinks: (the chromosome nb start and end are identical...)
gene_id bundle_id chr left right FPKM FPKM_conf_lo FPKM_conf_hi
ENSDARG00000000189 1367344 Zv8_scaffold3091 65836 148200 0.03 0 0.1
ENSDARG00000000189 1367346 Zv8_scaffold3091 65836 148200 0.03 0 0.1
ENSDARG00000000189 1367388 Zv8_scaffold3091 65836 148200 0.32 0.12 0.52
ENSDARG00000000189 1367400 Zv8_scaffold3091 65836 148200 0.29 0.1 0.48
ENSDARG00000000189 1367408 Zv8_scaffold3091 65836 148200 0.54 0.28 0.81
ENSDARG00000000189 1367410 Zv8_scaffold3091 65836 148200 0.38 0.16 0.6
ENSDARG00000000189 1367412 Zv8_scaffold3091 65836 148200 0.89 0.56 1.23
ENSDARG00000000189 1367414 Zv8_scaffold3091 65836 148200 0.54 0.28 0.81
ENSDARG00000000189 1367416 Zv8_scaffold3091 65836 148200 0.77 0.45 1.08
ENSDARG00000000189 1367418 Zv8_scaffold3091 65836 148200 0.48 0.23 0.73
ENSDARG00000000189 1367420 Zv8_scaffold3091 65836 148200 0.16 0.02 0.3
ENSDARG00000000189 1367424 Zv8_scaffold3091 65836 148200 0.06 0 0.15
ENSDARG00000001712 1367600 Zv8_scaffold3094 66975 111170 0.14 0 0.33

I realised that this is happening almost exclusively when the transcripts are mapped to the scaffold genomic location (ie the genome I use is not as good as the mouse and as still some parts which are not assembled into chromosome).

Cheers

Oliviera
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