View Single Post
Old 01-06-2013, 10:22 PM   #15
chayan
Member
 
Location: USA

Join Date: Nov 2012
Posts: 51
Default

Dear Blanca,
I talked to the MIRA mailing list and Bastien recomends me to use the XML files as well for MIRA. He also informed that in the latest version of seq_crumbs package mate-splitting tools are also mising. Additionallly, yes MIRA can use clipped data btu for a better amd more accurate result XML is also required specially when working with Ion torrent data,
Here's why
"E.g.: assume a sequence without left clips, but with two right clips. The quality clip at 15, the adaptor clip at 52 (visualised with spaces in the next line)

GTACGATCGAAAAA aaaaaaaaaaattttttttttttttttttttaaaaaa gtgtgtgtgt

Now, Ion has sometimes interesting homopolymer artefacts (not homopolymer errors, but artefacts like above) and MIRA makes sure they get completely clipped. I.e., for MIRA the above sequence become to

GTACGATCG aaaaaaaaaaaaaaaattttttttttttttttttttaaaaaa gtgtgtgtgt

Note that one of the clips advanced by 5 bases to the left, clipping it another couple of bases and completely hiding the Ion artefact. Now, if people use clipped sequence only, all MIRA would see is:

GTACGATCGAAAAA

Note how the homopolymer artefact, which was not entirely clipped in the SFF, now still contributes with 5 A to the sequence, and here MIRA is absolutely unable to see the true nature of those (most of the time) totally wrong A bases."
this was elustrated to me by Bastien

Thanks
chayan
chayan is offline   Reply With Quote