juliema
commented
2 years ago when you want to assemble each gene in a single fasta file you want you use the -Q rather -q to specify the query file. the capital Q tells atram to assemble each one sequentially.
Is that what you did initially?
On Sat, May 14, 2022 at 8:39 AM Upasana1991 @.***> wrote:
Hi I am Upasana I have 200 genome of anopheles sequenced at 30X I have a list of single copy orthologs that I have generated using proteomes of two reference genomes in Orthofinder. This gave me around 8322 single copy orthologs (list of amino acid sequence (.fa) files) I went through the tutorial of aTRAM and was clear to me how each step was written. In the example you have used only one .pep.fasta file ; When I used one amino acid sequence as. Target file, it worked, however When I concatenated all the .fa files into one sinlge .fasta file containing 11548 a.a sequences and used this as target file it didn’t work. Is there a way I can use the list of .fa file from orthofinder results as is? Is there a correct way of putting all the .fa files into one fast file ? I used this command “cat *.fa > TargetSCO.fasta”
Thanks for your time and help
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Upasana1991
Hi I am Upasana I have 200 genome of anopheles sequenced at 30X I have a list of single copy orthologs that I have generated using proteomes of two reference genomes in Orthofinder. This gave me around 8322 single copy orthologs (list of amino acid sequence (.fa) files) I went through the tutorial of aTRAM and was clear to me how each step was written. In the example you have used only one .pep.fasta file ; When I used one amino acid sequence as. Target file, it worked, however When I concatenated all the .fa files into one sinlge .fasta file containing 11548 a.a sequences and used this as target file it didn’t work. Is there a way I can use the list of .fa file from orthofinder results as is? Is there a correct way of putting all the .fa files into one fast file ? I used this command “cat *.fa > TargetSCO.fasta”
Thanks for your time and help