Post by djoser-xyyman on Dec 27, 2014 19:11:21 GMT -5
As I said, many aDNA geneome is available if you write to the resreachers and ask for it. Of course it is not as easy as that. They will check your credentials. Irregardless once you obtain the genome of these individuals you can "do your thing". These files are usally in the BAM or SAM file format. You then need the software to "read" the data.
I have in my possession BAM files for a few ancient(eg Otzi). I have the software also, but I need time to really get into to it.
You can to!
======
www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/
Working with BAM files
www.ncbi.nlm.nih.gov/...
National Center for Biotechnology Information
Aug 21, 2014 - This tutorial will take you through the several scenarios demonstrating BAM files in Genome Workbench. The 4 scenarios demonstrated are:.
===
Working with BAM Files
Step 1: Introduction
This tutorial will take you through the several scenarios demonstrating BAM files in Genome Workbench. The 4 scenarios demonstrated are:
• A sorted BAM file with index and coverage graph
• A sorted BAM file with index and no coverage graph
• A sorted BAM file with no index and no coverage graph
• A unsorted BAM file with no index and no coverage graph
The last two examples require you to have SAMTools installed and available. SAM Tools can be downloaded here:
samtools.sourceforge.net
Since BAM files can be VERY large, they are not loaded into the gBench project as other types of data and exist externally. Example files for this tutorial can be downloaded here (note the file is large ~365MB):
BAM Test Files
Step 2: Getting Started
From the File menu choose Open and select BAM/CSRA files from the left side.
Step 3: Viewing the BAM Data
Now you should have a track in the graphical view titled "mapt.NA12156.altex" and it is a blue graph. All the standard Genome Workbench navigation tools are available for panning and zooming (see Basic Operation tutorial).
I have in my possession BAM files for a few ancient(eg Otzi). I have the software also, but I need time to really get into to it.
You can to!
======
www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/
Working with BAM files
www.ncbi.nlm.nih.gov/...
National Center for Biotechnology Information
Aug 21, 2014 - This tutorial will take you through the several scenarios demonstrating BAM files in Genome Workbench. The 4 scenarios demonstrated are:.
===
Working with BAM Files
Step 1: Introduction
This tutorial will take you through the several scenarios demonstrating BAM files in Genome Workbench. The 4 scenarios demonstrated are:
• A sorted BAM file with index and coverage graph
• A sorted BAM file with index and no coverage graph
• A sorted BAM file with no index and no coverage graph
• A unsorted BAM file with no index and no coverage graph
The last two examples require you to have SAMTools installed and available. SAM Tools can be downloaded here:
samtools.sourceforge.net
Since BAM files can be VERY large, they are not loaded into the gBench project as other types of data and exist externally. Example files for this tutorial can be downloaded here (note the file is large ~365MB):
BAM Test Files
Step 2: Getting Started
From the File menu choose Open and select BAM/CSRA files from the left side.
Step 3: Viewing the BAM Data
Now you should have a track in the graphical view titled "mapt.NA12156.altex" and it is a blue graph. All the standard Genome Workbench navigation tools are available for panning and zooming (see Basic Operation tutorial).