Re: [Bammds-users] bammds

[Anna-Sapfo]

Hello Niall,
We would like to fix the bug so it works with your file as well.
Could you just copy paste the header of your bam file (samtools view -H)?

I will upload our reference to an ftp site for you but its a busy day so 
i dont know if i will get to it today.

Thanks!
anna

On 25-09-2014 17:18, OSullivan Niall wrote:
> I can't, the data is far too confidential to be circulated now.
>
> The genome was downloaded from here 
> http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/
>
> Best
>
> Niall
>
> -----Original Message-----
> From: address@hidden [mailto:address@hidden On Behalf Of Ole Tange
> Sent: giovedì 25 settembre 2014 16.48
> To: OSullivan Niall
> Cc: address@hidden
> Subject: Re: bammds
>
> On Thu, Sep 25, 2014 at 4:39 PM, OSullivan Niall <address@hidden> wrote:
> > Hi
> > I think it may be the reference file that was used for the bwa mapping. I used 
> > HG19 and I downloaded it directly from UCSC. You used a different one, but from 
> > where?
> Can you give me access to all the data you used, so I can reproduce your 
> problem? And a link to the HG19 file you used.
>
>
> /Ole