From FastQ to fasta - WGS Variant Analysis

variant
workflow
wgs
#1

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

1 Like
#2

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.

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

Thanks!

#3

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

1 Like