RE: Gene list headers

lkchan

Hi,

I am learning to use the DepthofCoverage function to obtain the gene coverage information for a collection of bacterial contigs that were mapped with metagenomic reads. The original post introducing this function is here: http://gatkforums.broadinstitute.org/discussion/40/depthofcoverage-v3-0-how-much-data-do-i-have#latest

In the post, you mentioned the gene list, as follow:

-geneList /path/to/gene/list.txt

The provided gene list must be of the following format:

585     NM_001005484    chr1    +       58953   59871   58953   59871   1       58953,  59871,  0       OR4F5   cmpl    cmpl    0,
587     NM_001005224    chr1    +       357521  358460  357521  358460  1       357521, 358460, 0       OR4F3   cmpl    cmpl    0,

I have three inquiries:

1. Can you please provide headers to the values in each column?
2. I am working with bacterial genomic contigs, can you please specify what basic information is needed for a gene list (e.g., name of contig, name of gene, location of gene in the contig, from... to ..., etc.)?

Thanks so much!

Leo

Geraldine_VdAuwera

This article explains how to work with refseq gene lists:

http://www.broadinstitute.org/gatk/guide/article?id=1329

lkchan

Hi Geraldine, Thanks. I am working on a genome assembled from metagenomes. So, I do not have refseq for this "genome". I have contigs and coding regions predicted from the contigs. I mapped the metegenomic raw reads to the contigs and would like to get coverage for all genes. I would have to generate a custom gene list. Thanks! Leo