Hi all,
I have made a RNA-seq experiment with the following features:
- Samples from Mus musculus
- ~20 millons of single-end reads, 75 pb length (good quality)
- Tecnology Illumina 1.9
Now I need to find the virus integration sites that have been inserted into
the genome of our mouse model. The genomic virus sequence is known. I have tried many procedures to locate that site with no success. Those procedures were:
- Generate the data base (consensus sequence) with Samtools tool, using
the reads mapped with lax parametres (BWA tool). Then I tried to find
the virus sequence in it (Blast tool).
- The Novo Assembly (Trinity tool). Then I tried to find the virus sequence in
it (Blast tool).
- Tophat-fusion and FusionMap, including the known virus sequence as a fake chromosome in order to search for fusion events in the whole genome.
Any other ideas or hints to find out viral integration sites in data types as described above will be really welcome.
Thanks a lot in advance for your replies.
I have made a RNA-seq experiment with the following features:
- Samples from Mus musculus
- ~20 millons of single-end reads, 75 pb length (good quality)
- Tecnology Illumina 1.9
Now I need to find the virus integration sites that have been inserted into
the genome of our mouse model. The genomic virus sequence is known. I have tried many procedures to locate that site with no success. Those procedures were:
- Generate the data base (consensus sequence) with Samtools tool, using
the reads mapped with lax parametres (BWA tool). Then I tried to find
the virus sequence in it (Blast tool).
- The Novo Assembly (Trinity tool). Then I tried to find the virus sequence in
it (Blast tool).
- Tophat-fusion and FusionMap, including the known virus sequence as a fake chromosome in order to search for fusion events in the whole genome.
Any other ideas or hints to find out viral integration sites in data types as described above will be really welcome.
Thanks a lot in advance for your replies.
Comment