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10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
59 stars 6 forks source link

Sort paired end .bam before run bamtofastq? #185

Open Alvis-Jiang opened 6 months ago

Alvis-Jiang commented 6 months ago

Hi,

Thanks for developing this wonderful tool! I am now using it to convert the possorted_genome_bam.bam generated by Cellranger to the fastq. I am not sure if it is paired end, should I sorted the bam file before running bamto fastq? As I have used the unsorted bam file to generate fastq, and then used the fastq file for scvelo. The scvelo show that there are about 300000 duplicated cells out of 400000 cell in total, I am not sure if it is because of the barcodes in the fastq files? Could you kindly give me some guidance?

Thanks a lot Boyu