Help! Obtaining consensus sequence from Aligned BAM file
Hi!
I have just aligned a paired-end FastQ (R1 & R2) files to a published viral genome using Bowtie2. The end goal is to extract the aligning reads from this sample and obtain a consensus sequence. Then I'd like to eventually compare that sequence to a reference sequence (published) to compare the differences between the two (I basically want to see if there is any nucleotide variation between the two samples), to help with primer design.
So, I have never done this type of pipeline before and would just like some assistance on creating and obtaining a consensus sequence. I use usegalaxy.eu and not coding.
Thanks!
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You can post this over at Galaxy help forum to get galaxy specific answers.
If you are able to replicate the steps in this tutorial on Galaxy then it should work: Generating consensus sequence from bam file
If you have found out solution then do let me know because i want to do same
Please post as a new query. But before that make sure that all your efforts were unsuccessful and consider following instructions by Genomax @https://www.biostars.org/u/89214/ .