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:
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.
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:
Code:
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
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.
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