fastq file to bam file

[zhanglab2008]

My Nanopore data are fastq files but the input files need to be in bam format. Do you have a way to convert the fastq files to bam files? Or I can just use Samtools to do that. Thanks!

[kaichop]

FASTQ files are just raw sequence reads. You need to use a mapping software (for example, minimap2) to map to a reference genome to generate the BAM file.

On Thu, Sep 22, 2022 at 1:00 PM zhanglab2008 @.***> wrote:

My Nanopore data are fastq files but the input files need to be in bam format. Do you have a way to convert the fastq files to bam files? Or I can just use Samtools to do that. Thanks!

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[zhanglab2008]

Got it thanks!

[zhanglab2008]

I still can't get the bam file with the correct format when I used minimap2 and then samtools to sort and index the bam file. The problem is that the "chromosome" column is missing in the sam/bam file from minimap2. I tried to use both transcript and genome gif file to prepare the refgene file but there is no difference. Do you have a tutorial to guide me how to produce the bam file from the ONT full length cDNA reads? Thanks!

[huyustats]

Please download genome fasta file instead of gtf file when using minimap2. Here is the tutorial of minimap2: https://lh3.github.io/minimap2/minimap2.html. If you have more question about minimap2, please create an issue at https://github.com/lh3/minimap2. Thanks!

[zhanglab2008]

Thanks for the reply. I was able to get the output after I use the full genome fasta file as reference.