You can filter and stay with your high quality reads. I had the same problem
and playing with the sets of prinseq I solved the problem. Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
Microbial Biotechnology DepartmentFellow of http://obrasocial.lacaixa.es/
Antes de imprimir este mensaje piense bien si es realmente necesario
hacerlo.Before you print this e-mail, think well if it is really necessary.
El Jueves 28 de Mayo de 2015 13:49, Dietmar Fernandez
<dietmar.fernandez@xxxxxxxxxxxx> escribió:
#yiv2808667829 #yiv2808667829 -- _filtered #yiv2808667829
{font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv2808667829
{font-family:Tahoma;panose-1:2 11 6 4 3 5 4 4 2 4;}#yiv2808667829
#yiv2808667829 p.yiv2808667829MsoNormal, #yiv2808667829
li.yiv2808667829MsoNormal, #yiv2808667829 div.yiv2808667829MsoNormal
{margin:0cm;margin-bottom:.0001pt;font-size:12.0pt;}#yiv2808667829 a:link,
#yiv2808667829 span.yiv2808667829MsoHyperlink
{color:blue;text-decoration:underline;}#yiv2808667829 a:visited, #yiv2808667829
span.yiv2808667829MsoHyperlinkFollowed
{color:purple;text-decoration:underline;}#yiv2808667829
span.yiv2808667829EstiloCorreo17 {color:#1F497D;}#yiv2808667829
.yiv2808667829MsoChpDefault {} _filtered #yiv2808667829 {margin:70.85pt 3.0cm
70.85pt 3.0cm;}#yiv2808667829 div.yiv2808667829WordSection1 {}#yiv2808667829
Prior to performing de novo assembly, have you checked the quality of your
samples? Which coverage are you supposed to have? First of all I would have
done a FASTQC or PRINSEQ in order to check wether you obtain a high number of
duplicates. De: mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] En nombre de Rameez Mj
Enviado el: jueves, 28 de mayo de 2015 13:44
Para: mira_talk@xxxxxxxxxxxxx
Asunto: [mira_talk] medium error: Very High Average Coverage I am using MIRA
for the first time for a bacterial whole genome de novo assembly project. I
use ion torrent data with average read length163 bp with 4,675,076 reads and
the assembly aborts with error saying very high average coverage. How can I
solve this problem? If I have to cut down the data volume how to do that
without sampling bias. Another one comment by mira was "Skewed distribution".Is
there any way to view and analyse the portion of data which contribute
skewness? For reference purpose I am attaching the assembly log here with.
