hi,
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.
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.