How to convert fastq to bam?

Question

[Jimpix]

Hello! Can you suggest any way to convert fastq file to bam file?

thx in advance.

[rpolicastro]

Did you want to align your reads to the genome, or just have an unaligned BAM file?

[Jimpix]

I need to upload then that bam file into IGV, so aligned

Answer 1

[ATpoint]

The process is called alignment, tools for DNA-seq are usually something like bowtie2 or bwa mem for short (Illumina) reads, minimap2 for long reads, and for RNA-seq you need a splice-aware aligner, something like STAR or hisat2 comes to mind. Please google for the tools and read existing threads and online materials, this is probably the most fundamental task of NGS analysis and extensively described in like every beginner's tutorial.

Just google "NGS alignment tutorial", there are plenty of websites offering guidance.