TABLE 2.

Troubleshooting table.

Step	Problem	Possible reason	Solution
1	TopHat cannot find Bowtie or the SAM tools	Bowtie and/or SAM tools binary executables are not in a directory listed in the PATH shell environment variable	Add the directories containing these executables to the PATH environment variable. See the man page of your UNIX shell for more details
2	Cufflinks crashes with a ‘bad_alloc’ error Cufflinks takes excessively long to finish	Machine is running out of memory trying to assemble highly expressed genes	Pass the –max-bundle-frags option to Cufflinks with a value of < 1,000,000 (the default). Try 500,000 at first, and lower values if the error is still thrown
5	Cuffdiff crashes with a ‘bad_ alloc’ error Cuffdiff takes excessively long to finish	Machine is running out of memory trying to quantify highly expressed genes	Pass the –max-bundle-frags option to Cuffdiff with a value of < 1,000,000 (the default). Try 500,000 at first, and lower values if the error is still thrown
	Cuffdiff reports FPKM = 0 for all genes and transcripts	Chromosome names in GTF file do not match the names in the BAM alignment files	Use a GTF file and alignments that has matching chromosome names (e.g., the GTF included with an iGenome index)