search

virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
Other
131 stars 42 forks source link

Conflict between web visualization interface and circle files #66

Open zhang919 opened 4 years ago

zhang919 commented 4 years ago

Dear， I have used AmpliconArchitect to calculate ecDNA，and I got the output store in {sample}_circle.txt, It is look like this：

...... Segment 39 chr17 74733453 75044078 Segment 40 chr17 74733453 76457572 Segment 41 chr17 75044585 78286079 Segment 42 chr17 76541050 77220084 Segment 43 chr17 76780795 78286079 Segment 44 chr17 77872851 78286079 Segment 45 chr17 78287354 78478856 Segment 46 chr17 78287354 79554855 Segment 47 chr17 78287354 81053816 Segment 48 chr17 78287354 81207906 ....... Cycle=1;Copy_count=9.60186061557;Segments=38+ Cycle=2;Copy_count=2.59240798421;Segments=0+,29-,0- Cycle=3;Copy_count=2.53013132658;Segments=44+,45+ Cycle=4;Copy_count=2.30677955765;Segments=0+,59-,0- Cycle=5;Copy_count=2.17360863377;Segments=0+,25-,23-,22-,20-,18-,0- Cycle=6;Copy_count=2.15262218464;Segments=0+,78-,62-,0- Cycle=7;Copy_count=2.06741149778;Segments=0+,91-,0- Cycle=8;Copy_count=1.99686214899;Segments=0+,13-,0- Cycle=9;Copy_count=1.95527158385;Segments=0+,3-,0- ......

So, I know I have the circle3 include 44+ and 45+ located in chr17. Then I upload this file to http://genomequery.ucsd.edu:8800/ to visualization, but what puzzles me is the output graph show the ciecle3 located in chr8.

图片

So, Could you please give me more information about it. Thanks for your attention. Best. Zhang.

jluebeck commented 4 years ago

Hi Viraj,

After discussing with Zhang in a separate thread, I believe this is an issue caused by the cycle_visualization tool not supporting hg38 output from my fork. I have not yet tried to update this visualization method to support hg38.

Best, Jens