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Old 06-27-2011, 10:21 AM   #1
Location: United States

Join Date: Jun 2011
Posts: 49
Default a question about tophat and cufflinks


I have some questions about using tophat and cufflinks.

1. I want to ask if these tools can extract all transcript level from my input fastq sequence, like the microarray matrix.

2. I have downloaded a geo fastq sequence, size 1G, and use

tophat mm9 SRRXXX.fastq

got a warning like :

Warning: junction database is empty!

And the result .bam file only have 270k.

then I use cufflinks accepted_hits.bam

got result in transcripts.gtf, only have 10 rows.

So what is this problem?

Thanks so much.
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