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Added flags to create genomebam file with kallisto bus #184

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merged 2 commits into from
Jan 14, 2023

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ricomnl
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@ricomnl ricomnl commented Jan 4, 2023

kallisto bus has the following optional options:

--genomebam               Project pseudoalignments to genome sorted BAM file
-g, --gtf                     GTF file for transcriptome information
                              (required for --genomebam)
-c, --chromosomes             Tab separated file with chromosome names and lengths
                              (optional for --genomebam, but recommended)

This PR adds parameters to kb count so that one can use the --genomebam flag as well as a gtf file and optionally a chromosomes file to output a .bam file. A test is added to make sure the functionality works as intended.

@ricomnl
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ricomnl commented Jan 4, 2023

@sbooeshaghi @Lioscro this would be a useful addition IMO because BAM files are required for downstream tasks like genetic demultiplexing. Right now, one would have to use cellranger to get bam files. In addition, the PR would solve this previous issue #147

@Yenaled
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Yenaled commented Jan 13, 2023

@ricomnl I am the person currently making major upgrades to and maintaining kallisto. Thanks for the pull request. I have several updates I need to make first but I will try to merge this pull request when I can. Don't worry -- it's on my radar.

@Lioscro
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Lioscro commented Jan 14, 2023

As long as the commands printed from --dry-run looks reasonable, the changes lgtm.

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Yenaled commented Jan 14, 2023

@Lioscro all looks good to me; feel free to merge

@Lioscro Lioscro changed the base branch from master to devel January 14, 2023 17:01
@Lioscro Lioscro merged commit 7aabc4b into pachterlab:devel Jan 14, 2023
@Lioscro Lioscro mentioned this pull request Jan 14, 2023
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3 participants