How To Do Scaffolding Using Mira For Ion Torrent Data?

Question

[Arpitha Hebbar]

i am using MIRA for the assembly of ion torrent data and i generated contigs. that file contains stars/gaps and mismatches. before doing scaffolding should i remove those mismatches or gaps or i can use that directly? if i suppose to remove those gaps and mismatches how can i do? please can you help me ?

Answer 1

[lelle]

If it is ok to have gaps depends on the program you use in downstream analysis.

If you need contig sequeces without gaps you do not have to remove them yourself. Mira will produce a file called projectname_out.unpadded.fasta which does not contain gaps ( in contrast to projectname_out.padded.fasta.

[Arpitha Hebbar]

thank you ... i did get both padded and unpadded fasta files files... i will surely try with those... thank you once again for the help...