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10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
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Unable to convert 10x bam to fastq using bamtofastq and getting folder named as "MissingLibrary" #15

Closed biobug16 closed 4 years ago

biobug16 commented 4 years ago

Hi i have a quick question, i have few aligned bam files from single cell RNA Seq data. I want to regenerate fastqs from them. In order to do so i am using 10x's bamtofastq utility and I am also getting fastq files but in the specified path within a folder named “MissingLibrary_1_flowcellName”. I am not sure what does this mean? Why the generated folder is named as missing library. Does anybody have any idea about this?

The command I used is: bamtofastq possorted_genome_bam.bam ./sample Any help will be highly appreciated.

Thanks

pmarks commented 4 years ago

@biobug16 You'll get "MissingLibrary" in the name of the output folder in some cases when the original run of the pipeline was not able to determine a certain name for the input data. You can ignore this -- the fastq in the output directory should be fine.

Yijia-Jiang commented 2 years ago

@biobug16 You'll get "MissingLibrary" in the name of the output folder in some cases when the original run of the pipeline was not able to determine a certain name for the input data. You can ignore this -- the fastq in the output directory should be fine.

Then how do you set a certain name for the directory of output data? We don't want a missing library output directory with some random letters.