Adding assembled_file option assembly process

[JohnMCMa]

As we discussed in Teichlab/bracer#21 , when using 10X Genomics outputs, reads should be split by cell and then called their VDJ types using bracer assembly's --assembled_file option.

I suppose the main idea also applies to TraCeR, but tracer assembly doesn't have a similar function. This means I'll have to split the fastq, calculate fragment length and SD and run the entire VDJ assembly pipeline despite the cellranger vdj output files are already assembled. My rough calculation shows this increases the running time by 3-4X.

[mstubb]

Yes, this is a direct consequence of TraCeR being written prior to release of the 10x Genomics VDJ product. We’ll put this functionality on the to-do list but I’d be happy to accept a pull request that does this if you’d like to write one.

All the best,

Mike

On 6 Sep 2018, at 15:23, John Ma [email protected] wrote:

As we discussed in issue 21 in BraCeR, when using 10X Genomics outputs, reads should be split by cell and then called their VDJ types using bracer assembly's --assembled_file option.

I suppose the main idea also applies to TraCeR, but tracer assembly doesn't have a similar function. This means I'll have to split the fastq, calculate fragment length and SD and run the entire VDJ assembly pipeline despite the cellranger vdj output files are already assembled. My rough calculation shows this increases the running time by 3-4X.

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