Detection of chimeric HIV-Host transcripts

Question

[Mrist01]

I am trying to detect the presences of chimeric HIV-host transcripts in my bulk RNA-seq datasets (single-end reads). The current protocols I have found online seem to align reads to both a human reference and HIV reference at the same time using Bowtie. Then they take reads that aligned to both HIV and human then BLAST those reads against a concatenated Human+HIV genomes.

Does anyone know how I can align to two references at once and pick out the sequences that align to both HIV and Human references? I have used HISAT2 to align my reads to hg38 and HIV reference separately but I do not know how to do this at the same time and then pick out these sequences.

Thank you in advance.

Answer 1

[Pierre Lindenbaum]

Does anyone know how I can align to two references at once and pick out the sequences that align to both HIV and Human references? I have used HISAT2 to align my reads to hg38 and HIV reference separately but I do not know how to do this at the same time and then pick out these sequences.

cat human.fa hiv.fa > merge.fa

index merge.fa

re-map the reads on merge.fa

and then something like: Extracting chimeric reads from mapping

[Mrist01]

I did this but then I am un able to index the concatenated genomes. I get hisat2-build command not found. Haven't found a good answer on how to fix this problem.

Is there another way for me to index this file?

[Pierre Lindenbaum]

Haven't found a good answer on how to fix this problem.

the whole internet is full of explanations about how to fix command not found

https://www.google.com/search?q=linux+how+to+fix+command+not+found