BAMboozle bam to fastq

[mej54]

Hi,

First of all, thank you for creating such a great tool for data privacy! We are hoping to use this to submit some human donor data to a database for publication and really appreciate the utility. Do you have a recommended way for converting the BAMboozled bam files to raw fastq files for scRNA-seq data?

Thank you, Molly

[cziegenhain]

Hey Molly,

Thanks for your message and using BAMboozle! I personally like to use samtools fastq for this.

Just note that, samtools expects/needs the reads to come sorted with the reads of each pair adjacent, so if you have paired-end data you would need to perform a sort by query name before. You could do like this: samtools sort -@ 10 -n bamboozled_reads.bam | samtools fastq -1 bamboozled_read1.fq -2 bamboozled_read2.fq -0 /dev/null -s /dev/null

Let me know if you have any other questions.

Best, Christoph

On Tue, 22 Mar 2022 at 16:35, Molly Johnson @.***> wrote:

Hi,

First of all, thank you for creating such a great tool for data privacy! We are hoping to use this to submit some human donor data to a database for publication and really appreciate the utility. Do you have a recommended way for converting the BAMboozled bam files to raw fastq files for scRNA-seq data?

Thank you, Molly

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[Close-your-eyes]

I used cellranger bamtofastq for that purpose. It works but the Index reads in a separate fastq file are not restored. Maybe that's expectable. FYI: I then used to bamboozled fastq files to run cellranger count. Now I am comparing the UMI matrices generated with original fastq and bamboozled fastq. Any recommendation how to do that elegantly?