The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
RE: Gene list headers
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:
- Can you please provide headers to the values in each column?
- 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!