how to merge many .fa files to one single target file containing list of amino acids

[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

[juliema]

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 — Reply to this email directly, view it on GitHub <#311>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2AZ3QRNH3F63JFXO3HMX3VJ7CKZANCNFSM5V5XC32A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Upasana1991]

Yes thank you . From: juliema ***@***.***> Date: Monday, 16 May 2022 at 18:07 To: juliema/aTRAM ***@***.***> Cc: Upasana Singh ***@***.***>, Author ***@***.***> Subject: Re: [juliema/aTRAM] how to merge many .fa files to one single target file containing list of amino acids (Issue #311) 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 — Reply to this email directly, view it on GitHub <#311>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2AZ3QRNH3F63JFXO3HMX3VJ7CKZANCNFSM5V5XC32A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub<#311 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AQNETIDT3J5OOCEL2WU3CYDVKJ6EJANCNFSM5V5XC32A>. You are receiving this because you authored the thread.Message ID: ***@***.***>