cuffmerge warnings Warning: couldn't find fasta record for 'chr1_GL456211_random'!

Question

[jolin0701-dy]

I got a cuffmerge warning like this

Warning: couldn't find fasta record for 'chr1_GL456211_random'!

Warning: couldn't find fasta record for 'chr1_GL456221_random'!

Warning: couldn't find fasta record for 'chrUn_JH584304'!

Warning: couldn't find fasta record for 'chrX_GL456233_random'!

After search, I noticed that this is a common warning due to the inconsistent names.

It is a warning, not error. And it still gives me the output files.

My questions are:

1 is the output file incomplete or not?

2 If I do "$grep -v random genes.gtf > genes.grep.gtf" and then use this gtf file for cuffmerge, is it OK to do it?

3 How to fix these warnings

Thanks so much~~

Answer 1

[Devon Ryan]

1. It's complete. Were it not, then those warnings would be errors instead.
2. That will get rid of most of the warnings. The better solution would be to just download the fasta file that includes the unplaced contigs from UCSC.
3. See above