[mira_talk] Re: denovo results clarifications
- From: Stefano Ghignone <stefano.ghignone@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 26 Mar 2010 12:27:20 +0100
On 03/24/2010 05:34 PM, Stefano Ghignone wrote:
But I also verified that some contigs I previously got with v.2.9* are
no more present in the assembly: the bad news is that I PCR validated
and re-sequenced some of them and now I get that these sequences are
listed as debris.....
I'm trying to find out the reason of what I reported a couple of days ago...
Checking into the file *project*_int_clippings.0.txt, some of the
already validated and re-sequenced 454 reads show these situation:
load: changed qual. EQM15JM01A2C7J Left: 15 Right: 230
load: unchanged mask. EQM15JM01A2C7J Left: 0 Right: 246
proposed cutback 1a: left EQM15JM01A2C7J 15 -> 24
proposed cutback 1a: right EQM15JM01A2C7J 230 -> 196
skim detect: possible junk: EQM15JM01A2C7J [172,0
proposed cutback: left EQM15JM01A2C7J 196 -> 245
load: changed qual. EQM15JM01EZ3TG Left: 15 Right: 228
load: unchanged mask. EQM15JM01EZ3TG Left: 0 Right: 244
skim detect: possible junk: EQM15JM01EZ3TG [213,0
proposed cutback: left EQM15JM01EZ3TG 228 -> 243
load: changed qual. EQM15JM01C0Z6V Left: 15 Right: 170
load: unchanged mask. EQM15JM01C0Z6V Left: 0 Right: 199
proposed cutback 1a: left EQM15JM01C0Z6V 15 -> 34
skim detect: possible junk: EQM15JM01C0Z6V [93,0
proposed cutback: left EQM15JM01C0Z6V 127 -> 198
load: changed qual. EQM15JM01E6YH1 Left: 15 Right: 234
load: unchanged mask. EQM15JM01E6YH1 Left: 0 Right: 250
proposed cutback 1a: right EQM15JM01E6YH1 234 -> 207
skim detect: possible junk: EQM15JM01E6YH1 [192,0
proposed cutback: left EQM15JM01E6YH1 207 -> 249
load: changed qual. EQM15JM01CPVJ8 Left: 15 Right: 237
load: unchanged mask. EQM15JM01CPVJ8 Left: 0 Right: 253
proposed cutback 1a: right EQM15JM01CPVJ8 237 -> 235
skim detect: possible junk: EQM15JM01CPVJ8 [0,174
proposed cutback: left EQM15JM01CPVJ8 15 -> 17
proposed cutback: right EQM15JM01CPVJ8 61 -> 48
proposed cutback: EQM15JM01CPVJ8 killed, remaining length (31)
skim detect: possible junk: EQM15JM01CPVJ8 [31,0
How should I interpret these values and which are the settings I need to
tune to let such reads be included into the assembly?
I also included the sanger sequences which should cover the same dna
region, but they where excluded as well:
load: changed qual. 8-283f.ab1 Left: 15 Right: 865
load: unchanged mask. 8-283f.ab1 Left: 0 Right: 881
load: changed qual. 8-283r.ab1 Left: 15 Right: 930
load: unchanged mask. 8-283r.ab1 Left: 0 Right: 1008
load: changed minleft. 8-283f.ab1 Left: 15 -> 30
load: changed minleft. 8-283r.ab1 Left: 15 -> 30
proposed cutback 1a: left 8-283f.ab1 30 -> 33
skim detect: possible junk: 8-283f.ab1 [832,0
skim detect: possible junk: 8-283r.ab1 [900,0
proposed cutback: left 8-283f.ab1 865 -> 880
proposed cutback: left 8-283r.ab1 930 -> 1007
...it has been experimentally validated!!... :-(
Regards,
stefano
--
Dr. Stefano Ghignone
Istituto per la Protezione delle Piante, Sez. Torino - CNR
c/o Dpt. Plant Biology, University of Turin
V.le P.A. Mattioli, 25
I-10125 Turin
Italy
Phone: +39 011 6502927 ext. 48
Fax: +39 011 6705962
e-mail: stefano.ghignone@xxxxxxxx
MSN: ste.ghi@xxxxxxxxxxx
http://www.bioveg.unito.it
http://www.sppadbase.com
http://www.dinamycode.it/
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
