[Heisman]

You want this link: http://hgdownload.cse.ucsc.edu/golde...9/chromosomes/

You will want to download all of those files; they provide the following command which may work:

rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ .

So, create a directory to put the reference sequence (use "mkdir hg19_UCSC_referenceSequence", for example), then cd into it ("cd hg19_UCSC_referenceSequence"), and then run that above command. That may work.

[Kienan]

How to generate .sam header

Hi Heisman,

Thanks again for your help yesterday. I've downloaded all of the files from the link you provided and have also downloaded PICARD. Am not sure how to run PICARD at all though....

[Heisman]

Ok, you want to unzip all of them (if they are in a directory, go to the directory and type "gunzip *"), and then concatenate all of them together (I think cat * > hg19.fa will work). Then you will be ready to use picard. At that point I think you want to do:

java -jar /pathtopicard/CreateSequenceDictionary.jar R=/pathtoreference/hg19.fa O=/pathtooutput/hg19.dict