- The data is from this experiment : http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-822/
- I downloed a *.bam file of this experiment from ENA: ftp://ftp.sra.ebi.ac.uk/vol1/ERA066/ERA066395/bam/MCF7_E2-12h_tophat.bam.
It should be mapped by TopHat as it is indicated in the file name.
- Can I use this TopHat bam file as input of CoverageBed to count the read?
- If yes, which GTF/GFF file I should use ?
On the other hand,
- The Input:
- the same TopHat bam file, ftp://ftp.sra.ebi.ac.uk/vol1/ERA066/ERA066395/bam/MCF7_E2-12h_tophat.bam
- the control bam
- GTF file from
I run cufflinks ,cuffmerg and cuffdiff. But the result is no gene is significantly differentially expressed. Where did I do wrong ? How to improve?
THANK YOU VERY MUCH!