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metagentools / MetaCoAG

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
https://metacoag.readthedocs.io/en/stable/
GNU General Public License v3.0
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Computing abundance TSV #5

Closed jdwinkler-lanzatech closed 2 years ago

jdwinkler-lanzatech commented 2 years ago

Hi,

Thanks for your work on this tool, looks very useful. I do have a question about generating the abundance TSV file that is expected; do you have a way of generating that file easily that you recommend? I can probably re-use something from MaxBin2 if not.

jdwinkler-lanzatech commented 2 years ago

Ah, figured out a simple way using samtools coverage, so I think I'm set here.

mant-ux commented 2 years ago

@jdwinkler-lanzatech Hello, how do you get the abundance tsv file? I use the script in concoct.Input the bam file and contig file to get the abundance tsv, but it is troublesome. Sometimes the error is reported and I don’t know what’s going on. Can you share me your method? thank you very much！

JLUVicent commented 2 years ago

Hi, thank you for your question, I have met the same problem, how do you generate abundance tsv files？ I would appreciate it if you could tell me the detailed steps of generating abundance tsv files using SamTools Thank you!

Vini2 commented 2 years ago

Hi @mant-ux and @JLUVicent,

Thank you for pointing this out. I find it easy to use the contig option from CoverM to get the abundance file. I have updated the README file of MetaCoAG with the code used to generate the abundance .tsv file for a single sample in the section How to get the abundance.tsv file. You will get the abundance.tsv file in the format explained in Input Format section and it can be directly used in MetaCoAG.

Hope this helps.

Thank you!