I possess RNA-Seq data in fastq.gz format and I'm seeking guidance on transforming it into a suitable BigWig (.bw) format.
What steps or tools are recommended to convert FASTQ files to BigWig format for visualization and analysis purposes? Any insights or recommended protocols would be greatly appreciated
Hi Mito
you'll need some expertise in bioinformatics to get this road.
starting from fastq files, you'll need to extract data, normalize them, align them on a genome and count the transcripts...once it's done, you'll have a count matrix you'll be able to use for your BW construction.
all the best
fred
bigWig is a track format (https://genome.ucsc.edu/goldenPath/help/bigWig.html). It summarizes mapping read coverage. You need to map the FASTQ reads to a reference sequence first. Once you have the mappings in SAM or BAM format, you can create bigWig files. There are many ways to get bigWig from BAM. For example, this post on Biostars https://www.biostars.org/p/9555490/.
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