Hello guys, I was trying to convert my 2 paired end fastq files to aligned sorted bam and I was sucessful but my file doesnt contain the coverage nor consensus sequence, do you know how can I can achieve this?
I was working with galaxy, got the fastq files from ENA.
Thank you for you time!
Hello,
Coverage data can be calculated for BAM datasets using several tools. At http://usegalaxy.org, search in the tool panel with the keywords "bam coverage" or simply "coverage" (no quotes) to find these.
Assembly is different and doesn't always mean the same thing. Some tools generate an actual fasta consensus sequence and other describe the boundaries of the consensus sequence with respect to a reference genome/transcriptome. The type of input fastq and the final analysis goal make a difference in which tools are appropriate. For the primary choices, see the tool groups NGS: RNA Analysis, NGS: Du Novo, and NGS: Assembly. Other tools perform specific manipulations (example: BEDtools > GetFastaBed).
Even more tool choices are available in the Main Tool Shed for use in a local or cloud Galaxy.
If you want to share more about your analysis inputs and goals, we can help point you to tools that will work with that type of data. You can also review the suite of Galaxy tutorials here for guidance: https://new.galaxyproject.org/learn/
Thanks! Jen, Galaxy team
Hi Jennifer! Thanks for the support
I want the single nucleotide coverage and the consensus of reads aligned to my reference like this image 
Do you know how can I use galaxy to obtain the result of this image?
I am trying to fix 2 stop códons into the gene of a transporter and I need to know where I can add some nucleotide to fix it but it will only be possible if I know the exactly place of indels with enough coverage to allow the change.
Thank you again for you time! you are beautiful
