From FastQ to fasta - WGS Variant Analysis

[demaio]

Dear All,
I am attempting to analyze a genic locus starting from Whole genome sequencing data. I am a newbie in this field (to date I have always used specific software that provided directly to give a final result.

Now I need to analyze a specific genic sequence that I am not able to obtain with previously cited software, but I should use Galaxy (easier than linux with command line scripts).

I have fastQ files (by Illumina paired end) that I have firsly analyzed by using Trimmomatic and then align (with BWA) to a reference genome. So, I have obtained a .bam file. I am attempting to obtain the consensus fasta sequence from this file….is it possible? o I am skipped some steps???
I have been using Galaxy tools.

Thank you in advance for you help

[jennaj]

Hi - Is your goal to explore variation?

If so, please review the tools below and see these Galaxy tutorials for examples of complete analysis workflows that include intermediate tools.

• Common tools to use from the step you are at now can be reviewed/used at Public Galaxy servers such as Galaxy Main https://usegalaxy.org, Galaxy EU https://usegalaxy.eu, and Galaxy AU https://usegalaxy.org.au (All Public Galaxy servers: Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub). Try searching for tools by these keywords: pileup or variant or vcf.

• The Galaxy ToolShed Galaxy | Tool Shed can also be searched for tools that can be used in your own Galaxy instance https://galaxyproject.github.io/.

• GTN Tutorials: Variant Analysis

Galaxy Training: Variant Analysis

• More about how/where to use Galaxy GTN tutorials and the included tools/workflows for your own work.

@jennaj

Galaxy Training Network Tutorials : Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

Thanks!

[demaio]

Thanks a lot for your help

Correct, I am searching some indels in a specific genomic region. So I would like to firstly obatin fasta sequence, to analyze this region and finally, if necessary, to sequence by using sanger or anplicon based NGS.
Now I will try as suggested