Can I map reads to one chromosome at a time and then merge them together with `mapmerge?
No, you cannot. All the chromosomes of the reference genome should be put into a single FASTA file. Maq is designed in this way to avoid technical complexity. • The qualities of the 3′-end of my reads are not great. Should I trim them off? If you are using maq-0.6.0 or later, I usually do not recommend to do this because Maq is designed to cope with this case. However, if your reads show obvious compositional biases, trimming the reads (with `maq map -1 30′ for example) may be preferrable. If you think recursively trimming always works better, please let me know. Thank you. • Eland tells me the best hit has one mismatch, but the best hit found by Maq has two mismatches. What happens? Maq is quality-aware. Before alignment, Maq divides base qualities by 10 and then cuts off the decimal part. In alignment, hit A is said to be better than hit B if the sum of the 10-divided quality values of mismatched bases of A is smaller. Maq does not always favour the position yielding fewer mismatches
Related Questions
- The map is rather big and sometimes it takes a long time to finish the game head-to-tail. What shall we do if time is limited?
- Is there the ability to add local content to the map, either one point at a time or by uploading GIS or GPS files?
- Can I map reads to one chromosome at a time and then merge them together with `mapmerge?
