fastq file to bam file

Question

fastq file to bam file

Closed this issue 2 years ago · 5 comments

zhanglab2008 commented 2 years ago

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!

Answer 1 · 2022-09-22T17:50:00.000Z

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.

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Answer 2 · 2022-09-22T18:17:02.000Z

Got it thanks!

Answer 3 · 2022-09-23T14:56:57.000Z

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!

Answer 4 · 2022-09-23T15:01:49.000Z

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!

Answer 5 · 2022-09-26T02:26:24.000Z

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