sample_EXP_REFINEFINAL1.cmap

[cxshine]

How can I get the sample_EXP_REFINEFINAL1.cmap files?

[jluebeck]

The EXP_REFINEFINAL1.cmap file is generated by the Bionano de novo assembly pipeline, and located in their '/contigs/' output folder.

If you are searching for publicly available Bionano data, you can find many (including those used in the AR paper) here: https://ftp.ncbi.nlm.nih.gov/pub/supplementary_data/bionanomaps.csv

Best,
Jens

[Cathy94]

I run : $AR_SRC/generate_cmap.py -r /cluster/references/genome/human/GRCh37-lite.chr.fa -e DLE1 -g CT049_amplicon1_graph.txt
The CT049_amplicon1_graph_DLE1.cmap was generated, but I could not find CT049_EXP_REFINEFINAL1.cmap. How can I find '/contigs/' output folder? Thank you.

[jluebeck]

Did you generate CT049 Bionano data? In the output files you received from running the sample on the Bionano platform, you will see the contigs directory.

[Cathy94]

Sorry, I did not generate CT049 Bionano data. How can I recieve the CT049 Bionano data? | | 赵爽 | | ***@***.*** | ---- Replied Message ---- | From | Jens ***@***.***> | | Date | 4/20/2023 11:57 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [jluebeck/AmpliconReconstructor] sample_EXP_REFINEFINAL1.cmap (#3) | Did you generate CT049 Bionano data? In the output files you received from running the sample on the Bionano platform, you will see the contigs directory. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[jluebeck]

You would need to find someone who has those cells, find a Bionano service provider, and arrange for the cells to undergo Bionano imaging.