All,
I'm seeking your advice and suggestions to identify the viral genome from viral-infected patient sample sequenced on IonTorrent. A totol 0.34 million reads of length 5-202bp DNA reads was generated, out of which 0.30 million reads were selected after filtering low quality reads based on read length (<20bp), quality trim (Q<14 at 5', 3') and mean QV <14.
1) To substract the human background, the remaining reads were mapped to hg19 using Tmap, bwa, Bowtie2 using default params, provided different mapping results 45%, 10%, 12% respectively. But I see Tmap reported mapping even with say 18bp match in 200bp read, probably the reason for high mapping %. But all of them showed only 8-12% mapping with mapQ>8. What;s your opinion on this? Any other aligned I should try or any specific parameters?
2)Next, I would like to map the unmapped reads to ~4000 viral genome db from NCBI. How can I do this as I would get the % of reads mapped to each genome and get a summary of mapping. Which tool does suite best to this?
Anyone has any previous experience on this kind of analysis (with IonTorrent data)?
Thanks
Raj
I'm seeking your advice and suggestions to identify the viral genome from viral-infected patient sample sequenced on IonTorrent. A totol 0.34 million reads of length 5-202bp DNA reads was generated, out of which 0.30 million reads were selected after filtering low quality reads based on read length (<20bp), quality trim (Q<14 at 5', 3') and mean QV <14.
1) To substract the human background, the remaining reads were mapped to hg19 using Tmap, bwa, Bowtie2 using default params, provided different mapping results 45%, 10%, 12% respectively. But I see Tmap reported mapping even with say 18bp match in 200bp read, probably the reason for high mapping %. But all of them showed only 8-12% mapping with mapQ>8. What;s your opinion on this? Any other aligned I should try or any specific parameters?
2)Next, I would like to map the unmapped reads to ~4000 viral genome db from NCBI. How can I do this as I would get the % of reads mapped to each genome and get a summary of mapping. Which tool does suite best to this?
Anyone has any previous experience on this kind of analysis (with IonTorrent data)?
Thanks
Raj