AmpliconReconstructorOM CRAM support

Hello

I want to know if AR supports CRAM file as input? Thanks.

Oct 09 '20 17:10 xtmgah

Hi,

AR does not directly take a BAM/CRAM as input - only the AA-generated breakpoint graph derived from those files. AA is compatible with CRAM input, as per the AA README.

The workflow for analysis using AR involves running AA first, then running AR using that output along with the Bionano data.

Oct 09 '20 17:10 jluebeck

Hi,

AR does not directly take a BAM/CRAM as input - only the AA-generated breakpoint graph derived from those files. AA is compatible with CRAM input, as per the AA README.

The workflow for analysis using AR involves running AA first, then running AR using that output along with the Bionano data.

Could you please tell me something about the address? That l can find more cmap files, thanks. Now, l jump into the AR, but l can't find the cmap file.

Aug 23 '22 06:08 ZHONGHONGXIN

Hi, cmap files are generated from Bionano optical mapping. This is an entirely separate assay from whole-genome sequencing. The NCBI keeps a repository of Bionano OM data here.

Aug 25 '22 01:08 jluebeck

Hi, cmap files are generated from Bionano optical mapping. This is an entirely separate assay from whole-genome sequencing. The NCBI keeps a repository of Bionano OM data here.

Hi, jluebeck

l find the human lung camp file to replace the real sample camp file because l can find my sample cmap file; l get the eccDNA circle, but l don't know this result whether or not correct. Could you please tell me some advice, thanks?

HongXin

Aug 30 '22 10:08 ZHONGHONGXIN

Hi HongXin,

Sure, you can email me results at jluebeck [a t] ucsd.edu and I can take a look.

Jens

Aug 30 '22 15:08 jluebeck

Hi HongXin,

Sure, you can email me results at jluebeck [a t] ucsd.edu and I can take a look.

Jens

Thanks, l send an email to your adress just now.

Aug 30 '22 16:08 ZHONGHONGXIN