I have used BWA-mem2 for sample alignment with reference human pappiloma virus. The reference is not available on the Galaxy Europe platform, hence I uploaded the reference.
After successful alignment, when selecting the uploaded reference HPV16 genome using Galaxy history dataset on IGV, error 416 was shown.
How do I solve it?
Kindly answer as soon as possible.
I’m not sure @abhi_g, but your input dataset visible in the first screenshot above has a suspiciously small size of just 2.4kB. Could it simply be empty, i.e. not contain any mapped reads?
Thank you.
The reference genome that I have uploaded “GCF_000863945.3_ViralProj15505_genomic” is HPV16 and is only 7.9 KB while the sample “SRR35875587” is 2.5 KB. Hence, result may be 2.4KB.
Kindly suggest.
Can you share your history with me then for more detailed debugging?
I am trying to align the sample genomic sequence of Human papillomavirus virus sequence from target with the reference Human papillomavirus virus.
Because the reference is not able on Galaxy Europe platform, I uploaded the reference HPV16 “GCF_000863945.3_ViralProj15505_genomic” & “GCF_000863945.2_ViralProj15505_genomic” that I downloaded from NCBI.
This sample consists only of a single read!
It’s an assembled genome, not raw sequencing data.
bwa-mem is the wrong tool for this task. You just want to run a pairwise sequence aligner, like e.g. EMBOSS Needle with the two files as input.
There is also no need to create your own reference then, you simply upload the reference sequence as a dataset.
Thank you.
