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 ?
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Arpitha Hebbar
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.
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...
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