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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Error: the required database file annovar/AT_refGeneMrna.txt/hg18_refGene.txt does not exist. #226

Open tbestone opened 1 year ago

tbestone commented 1 year ago

Helllo guys, I am trying to run annovartable using this code: annovar/table_annovar.pl annovar/output.avinput annovar/AT_refGeneMrna.fasta annovar/AT_refGeneMrna.txt -out myanno -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp138,ljb23_all -operation g,r,r,f,f,f,f -nastring . But I am getting the error. Could you pls help me with this issue? I created the avinput file and mrna.fasta files using annovar.

kaichop commented 1 year ago

The table_annovar command takes an input file and examines a database directory to find necessary annotation files. In this case, you are probably trying to analyze human genome data, so you need to select a build (possibly hg19 or hg38), and I am not sure why you use " annovar/AT_refGeneMrna.fasta annovar/AT_refGeneMrna.txt" in the command line. Just read the quick start-up guide for instructions on how to use annovar. You probably do not want to use ljb23_all or snp138, since they are extremely old.

On Sat, Jul 22, 2023 at 6:56 AM tbestone @.***> wrote:

Helllo guys, I am trying to run annovartable using this code: annovar/ table_annovar.pl annovar/output.avinput annovar/AT_refGeneMrna.fasta annovar/AT_refGeneMrna.txt -out myanno -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp138,ljb23_all -operation g,r,r,f,f,f,f -nastring . But I am getting the error. Could you pls help me with this issue? I created the avinput file and mrna.fasta files using annovar.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/226, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGR54XTKUAJTGOJ43LXROWWRANCNFSM6AAAAAA2TYNBY4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

tbestone commented 1 year ago

Dear Wang thank you for your reply I am working on Apricot not human and I got MrnaGene.fasta and avinput files using annovar, next step I guess is to annotation using table_annovar. but I couldn't figure it out. Could you pls help me with this issue?

On Sun, Jul 23, 2023 at 2:39 AM Kai Wang @.***> wrote:

The table_annovar command takes an input file and examines a database directory to find necessary annotation files. In this case, you are probably trying to analyze human genome data, so you need to select a build (possibly hg19 or hg38), and I am not sure why you use " annovar/AT_refGeneMrna.fasta annovar/AT_refGeneMrna.txt" in the command line. Just read the quick start-up guide for instructions on how to use annovar. You probably do not want to use ljb23_all or snp138, since they are extremely old.

On Sat, Jul 22, 2023 at 6:56 AM tbestone @.***> wrote:

Helllo guys, I am trying to run annovartable using this code: annovar/ table_annovar.pl annovar/output.avinput annovar/AT_refGeneMrna.fasta annovar/AT_refGeneMrna.txt -out myanno -remove -protocol

refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp138,ljb23_all

-operation g,r,r,f,f,f,f -nastring . But I am getting the error. Could you pls help me with this issue? I created the avinput file and mrna.fasta files using annovar.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/226, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNG3OGR54XTKUAJTGOJ43LXROWWRANCNFSM6AAAAAA2TYNBY4>

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kaichop commented 1 year ago

If your genome build is called "AT", then you need to use -buildver AT in the command. You can only do gene-based annotation, because all the other databases are for human genomes.

Assuming that the AT_refGeneMrna.fasta and AT_refGeneMrna.txt files are stored in the "annovar" directory, then you just use annovar/table_annovar.pl annovar/output.avinput annovar/ -buildver AT -out myanno -remove -protocol refGene -operation g -nastring .

On Sun, Jul 23, 2023 at 2:37 AM tbestone @.***> wrote:

Dear Wang thank you for your reply I am working on Apricot not human and I got MrnaGene.fasta and avinput files using annovar, next step I guess is to annotation using table_annovar. but I couldn't figure it out. Could you pls help me with this issue?

On Sun, Jul 23, 2023 at 2:39 AM Kai Wang @.***> wrote:

The table_annovar command takes an input file and examines a database directory to find necessary annotation files. In this case, you are probably trying to analyze human genome data, so you need to select a build (possibly hg19 or hg38), and I am not sure why you use " annovar/AT_refGeneMrna.fasta annovar/AT_refGeneMrna.txt" in the command line. Just read the quick start-up guide for instructions on how to use annovar. You probably do not want to use ljb23_all or snp138, since they are extremely old.

On Sat, Jul 22, 2023 at 6:56 AM tbestone @.***> wrote:

Helllo guys, I am trying to run annovartable using this code: annovar/ table_annovar.pl annovar/output.avinput annovar/AT_refGeneMrna.fasta annovar/AT_refGeneMrna.txt -out myanno -remove -protocol

refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp138,ljb23_all

-operation g,r,r,f,f,f,f -nastring . But I am getting the error. Could you pls help me with this issue? I created the avinput file and mrna.fasta files using annovar.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/226, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABNG3OGR54XTKUAJTGOJ43LXROWWRANCNFSM6AAAAAA2TYNBY4>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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