Aligner like BWA consider it a straightened reference, starting from 0 and ending at the end coordinate. Now the issue is with the reads which are starting from some tail ending coordinate and forming overhang. Samtools usually ask for removal of these reads. How can I not lose this data. One outcome was to extend the reference with some reads from the 0th coordinate to say up to 50 base. What would be with the reads which were only mapping in that region? It would form dual mapping. Any suggestion?
I presume the easiest would be to add artificially to the end of the genome the very beginning, to the maximum read length. That way you do not lose any information.
I took that strategy only, but smaller reads which were specifically mapping at the starting end are now mapping twice....Once at its original position, and once in the added tail end. What to do now?
You have the Bowtie option to assign a read only once, randomly. -M 1 I think. That should sort this problem out.
Thanks for the comments. But I have found Novoaligner, which actually take care of this issues...
@NavonilDeSarkar. Can you give the link that explains that Novalign manages this issue ?
I would like to find out also how to use Novoalign to align to circular genome?
- Badges
- Science method