Good morning SeqAnswers community,
Today I am interested in adding a "locus" column to my diff_genes.txt file. I'm refering to the code at the top of pg. 575 in the 2012 Nature Protocol by Trapnell et al.
>gene_diff_data<-diffData(genes(cuff_data))
>sig_gene_data<-subset(gene_diff_data, (significant=='yes'))
>write.table(sig_gene_data, 'diff_genes.txt', sep='\t', row.names=F, col.names=T, quote=F)
The so called "locus" column is found in the genes_exp.diff file in the cuffdiff output. Again, I would like to capture this column in my diff_genes.txt. Furthermore, I would really like to have a column of "/product" ID's from the original GeneBank file, but that seems like it would involve a VBA script that would search the GeneBank file for the "locus tag" and then copy what's in quotations 5 rows down from it. I don't remember how to do that anymore though, so if anyone has any ideas before I manually ctrl find all my locus tags and product ID's, I'd really appreciate the help.
I found this, but I don't know if it is relevant since there are no examples.
4.1 Adding additional feature annotation
Gene- or feature-level annotation can be permanently added to the database tables for future querying. If you have a data.frame where the first column contains the 'tracking_id' (eg. 'gene_id' for genes, 'isoform_id' for isoforms, etc). You can easily add feature level annotation using the addFeatures() function:
> annot<-read.table("gene_annotation.tab",sep="\t",header=T,na.string="-")
> addFeatures(cuff,annot,level="genes")
By default, features added to a CuffSet object are assumed to be gene-level annotations, but the level can selected using the argument level. Features added to a CuffData object are assumed to be of the same type as the 'type' value for that given object (e.g. gene-level features for 'genes', isoform-level features for isoforms, etc.) - See more at: http://compbio.mit.edu/cummeRbund/ma....mojSSK12.dpuf
Thanks and God bless,
Jason
Today I am interested in adding a "locus" column to my diff_genes.txt file. I'm refering to the code at the top of pg. 575 in the 2012 Nature Protocol by Trapnell et al.
>gene_diff_data<-diffData(genes(cuff_data))
>sig_gene_data<-subset(gene_diff_data, (significant=='yes'))
>write.table(sig_gene_data, 'diff_genes.txt', sep='\t', row.names=F, col.names=T, quote=F)
The so called "locus" column is found in the genes_exp.diff file in the cuffdiff output. Again, I would like to capture this column in my diff_genes.txt. Furthermore, I would really like to have a column of "/product" ID's from the original GeneBank file, but that seems like it would involve a VBA script that would search the GeneBank file for the "locus tag" and then copy what's in quotations 5 rows down from it. I don't remember how to do that anymore though, so if anyone has any ideas before I manually ctrl find all my locus tags and product ID's, I'd really appreciate the help.
I found this, but I don't know if it is relevant since there are no examples.
4.1 Adding additional feature annotation
Gene- or feature-level annotation can be permanently added to the database tables for future querying. If you have a data.frame where the first column contains the 'tracking_id' (eg. 'gene_id' for genes, 'isoform_id' for isoforms, etc). You can easily add feature level annotation using the addFeatures() function:
> annot<-read.table("gene_annotation.tab",sep="\t",header=T,na.string="-")
> addFeatures(cuff,annot,level="genes")
By default, features added to a CuffSet object are assumed to be gene-level annotations, but the level can selected using the argument level. Features added to a CuffData object are assumed to be of the same type as the 'type' value for that given object (e.g. gene-level features for 'genes', isoform-level features for isoforms, etc.) - See more at: http://compbio.mit.edu/cummeRbund/ma....mojSSK12.dpuf
Thanks and God bless,
Jason