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Old 08-10-2010, 06:55 PM   #1
repinementer
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Location: asia

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Default Tophat Junction reads are very low comapred to ERANGE

Does any one know why the number of junction reads of TopHat (117410) are very less compared to ERNAGE. It should be more than ERANGE I suppose ?

And the genomic reds number is more than the original reads? (32233301)

I ran Illumina solexa single end rnaseq reads

BLAT+ERANGE
Samples No. Reads Genomic reads Genomic reads Junction reads
Adipose 27752231 17.6 M (unique) 4.8 M (non-unique) 1.4MB


BOWTIE+TOPHAT

Samples No. Reads Genomic reads Junction reads
Adipose 27752231 32233301 117410
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Old 08-11-2010, 02:41 AM   #2
Thomas Doktor
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Could you give us a bit more information about how you count the number of reads?
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