identification of viral gene from fastq or BAM file

Question

[kay]

Hello,

I have a fastq and BAM file for a viral genome sample (obtained from NGS data). I want to identify viral genes from this sample.

I saw a "virusSeq" - but this seems to screen only for a small number of viruses.

I also tried cufflinks, but all the FPKM values were 0.

Not sure what to do. Any suggestions for methods?

Thanks
K

[Asaf]

Cufflinks didn't work because you didn't map the reads to a viral genome

[kay]

I already did all that. I took the viral fastq files, and mapped it to viral reference using BWA and have a viral BAM file. I also have .gff files about the viral genes from NCBI.

I input the viral BAM file and the .gff file into cufflinks, but all FPKM values are 0.

[Asaf]

OK, that's weird, what was the mapping rate?

[kay]

When you say "mapping rate" what do you mean ? When I aligned to genome using BWA, the % of alignment was > 80%

[Prakki Rama]

You want viral genes from the fastq file? I do not think it is possible. You need to have contigs first which are assembled from your fastq file. Then align the contigs to the reference viral genes. Then you should be able to identify. Else, If you want viral reads, from your fastq, then try aligning the fastq reads to the reference viral genes using tools like BLAT or May be you need to tweak the parameters while using cufflinks.

[bioinforesearchquestions]

Hi Krithika,

Even, I am working on the same task. I need to extract gene sequences from the NGS sequenced reads. Also, I am interested in generating a phylogenetic tree for many samples.

Can you please provide some background on it?