Always run into problems with Cuffmerge

[DonDolowy]

Hi everyone,

I always encounter problems when using Cuffmerge saying that it cannot find specific fasta records.

I have downloaded both USCS mm9 and ENSEMBL from iGenomes, run top hat, cufflinks followed by cuffmerge.

The command:

cuffmerge -g /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.grep.gtf -s /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -p 8 assemblies.txt

When I use mm9 I get:
Warning: couldn't find fasta record for 'chr13_random'!
Warning: couldn't find fasta record for 'chr17_random'!
Warning: couldn't find fasta record for 'chr1_random'!
Warning: couldn't find fasta record for.......

When I use Ensembl, I get similar problems:


Do you know what is going on here? I have tried to use grep command to remove all lines containing 'random' from the genes.gtf from mm9 iGenomes, but I am not sure if this is the way to do it.

Thanks a lot!

I really appreciate your help.

[jp.]

did you get any solution for this problem ?

Hi everyone,

I always encounter problems when using Cuffmerge saying that it cannot find specific fasta records.

I have downloaded both USCS mm9 and ENSEMBL from iGenomes, run top hat, cufflinks followed by cuffmerge.

The command:

cuffmerge -g /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.grep.gtf -s /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -p 8 assemblies.txt

When I use mm9 I get:
Warning: couldn't find fasta record for 'chr13_random'!
Warning: couldn't find fasta record for 'chr17_random'!
Warning: couldn't find fasta record for 'chr1_random'!
Warning: couldn't find fasta record for.......

When I use Ensembl, I get similar problems:


Do you know what is going on here? I have tried to use grep command to remove all lines containing 'random' from the genes.gtf from mm9 iGenomes, but I am not sure if this is the way to do it.

Thanks a lot!

I really appreciate your help.

[DonDolowy]

I am just using the the grep´ed version of the genes.gtf where I have removed chr_random entries.

[jp.]

Can you please tell me in a bit more detail (commands) because I am new in this field.
Thank you

I am just using the the grep´ed version of the genes.gtf where I have removed chr_random entries.

[DonDolowy]

I am using UCSC mm9 genes.gtf from iGenome.

I imagine I did something like:

grep -v random genes.gtf > genes.grep.gtf