Open mej54 opened 2 years ago
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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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?
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