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BioAlgs / MetaGen

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Easy way to use existing mapping data (bam-files) #4

Open jvollme opened 5 years ago

jvollme commented 5 years ago

If I want to use multiple binning tools and then integrate their results (e.g. Using das tool), I often have read data already available in form of bam files and redoing the mapping for MetaGen would be a nuisance. Also in some cases, metagenomic samples had to be resewuenced multiple times, resulting in multiple fastq-files for one sample. MetaGen would currently require concatening these files, which is a nuisance if one could alternatively use mapping results that treat these reads as one sample already.

Therefore, is there an easy way to use existing mapping data (in form of bam files) to extract and give MetaGen its required coverage info? Could this perhaps even be included as an direct option of MetaGen.sh (feature request)?

BioAlgs commented 5 years ago

If you do not want to concatenate the fastq files, you can concatenate the columns of the extracted read count mapping matrix. I think this will be more convenient.

On Wed, May 22, 2019 at 6:36 AM JohnVollmers notifications@github.com wrote:

If I want to use multiple binning tools and then integrate their results (e.g. Using das tool), I often have read data already available in form of bam files and redoing the mapping for MetaGen would be a nuisance. Also in some cases, metagenomic samples had to be resewuenced multiple times, resulting in multiple fastq-files for one sample. MetaGen would currently require concatening these files, which is a nuisance if one could alternatively use mapping results that treat these reads as one sample already.

Therefore, is there an easy way to use existing mapping data (in form of bam files) to extract and give MetaGen its required coverage info? Could this perhaps even be included as an direct option of MetaGen.sh (feature request)?

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