hi i have followed pipeline grooming the sra data followed by tophat and cufflink.cuffdiff job is taking too long.i want to know that is their some error in my input to cuffdiff.what i should check in cufflink result.how to see the result of tophat is satisfactory or not
To validate if your tophat worked(i.e.the reads aligned correctly to the reference genome), you can try:
Visualizing regions of interest in the genome. This can be done using Tracker or browsers such as Integrated Genome Browser(IGB) or Integrative Genomics Viewer(IGV) by expanding your tophat "accepted_hits" files, and clicking on either: "display with IGV" or "display in IGB View."
You can also check your mapping statistics by accessing the "align_summary" file.
This means that tophat did not work. Only 1226 reads out of 19118751 reads were aligned to the reference genome, hence 0.0% of input.
Double check if you had provided the correct reference genome. Did you run a quality check on your reads (i.e. fastQC)? This will allow you to see if the reads are of good quality, with which you can decide whether you need to manipulate the reads or filter out poor quality reads. Every part of the fastQC results is described in the link provided: