HIV NL4-3 transcriptome fasta

Question

[xiaoleiusc]

Hi, All,

I wonder is there a place which I can download HIV NL4-3 transcriptome Fasta file as a reference file in my NGS RNA reads mapping? Although I know how to use the HIV NL4-3 genome as a reference file, however, I am particularly interested in the reads that are generated from HIV RNA splicing, so I think it would be better if I could map my reads to NL4-3 transcriptome which have all the spliced sequences. What I would like to do is first align my reads to HIV genome (unspliced reads), and then extract the unmapped reads and align the unmapped reads to HIV transcriptome to find the spliced reads.

Thanks ahead,

Xiao

Answer 1

[Prisca :)]

Hi Xiao,

Were you able to make progress on this? If so, could you share what you did/found?

[xiaoleiusc]

Hi, Prisca, Unfortunately no progress on this. I could not find a database with NL4-3 splicing transcriptome.

Best, Xiao