How could I use the Ensembl ncRNA fasta file to annotate my RNA-seq data

Question

[i19870503]

I have use tophat and cufflinks get the out put, but I do not understand how to use ncRNA fasta file (from Ensembl database) annotate the results.

BTW, I use the genome from UCSC, the GTF file from the Ensembl (as the annotation of pig is not sufficient in UCSC table browser). When I run cuffmerge I get lots of warnings, such as :

Warning: couldn't find fasta record for 'chrGL895457.1'!
This contig will not be bias corrected.

Is that have some bad influence on the results?

[Manvendra Singh]

Yes, This is the problem.

Its always recommended to use genome and GTF from the same source.

Otherwise you will have to remove all those rows from GTF which does not have fasta records.

HTH

Answer 1

[devrishi]

UCSC add a chr to the standard record names, so you would need to add this prefix as appropriate to the Ensembl GTF. Or you can use the genome from Ensembl. ftp://ftp.ensembl.org/pub/release-77/fasta/sus_scrofa/dna/

[Manvendra Singh]

I think that the ensembl gtf she is using has 'chr' prefix

[i19870503]

you are right, I have already add the 'chr' and then run the cufflinks.