Description

Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

bam (file)

BAM file

*.bam

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

fastq (file)

fastq compressed file

*.fastq.gz
maintainer
Github user BlueBicycleBlog
get in touch
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Tools

bamtofastq10x
MIT

Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis

github.com/10XGenomics/bamtofastq