Thank you very much Andrej,
As it seems SPades for a reason that I cannot understand cuts the
identification of the pair.
Vasilis.
On May 8, 2015, at 3:35 PM, Andrej Benjak <abenjak@xxxxxxxxx>
wrote:
Hi Vasilis,
If these are PEs, the read names for each pair should look like this:
@HWI-D00173:80:C42H0ACXX:8:1101:1295:2161/1
@HWI-D00173:80:C42H0ACXX:8:1101:1295:2161/2
or:
@HWI-D00173:80:C42H0ACXX:8:1101:1295:2161 1:<whatever...>
@HWI-D00173:80:C42H0ACXX:8:1101:1295:2161 2:<whatever...>
And make sure you define them as as PEs in the manifest.
(I am not sure if MIRA would accept PEs without the above naming scheme.)
Andrej
On 05/08/2015 04:24 PM, lenis vasilis wrote:
Hello everyone,
I'm running Mira in reference based mode and I face the following problem:
Read HWI-D00173:80:C42H0ACXX:8:1101:1295:2161 is present more than once in
the data set. Did you load a file twice in the manifest? Is a read present
more than once in your file(s)?
……..
More than 2000 cases like the above, will not report more. Fix your input!
This problem occurred when I tried to run Mira with fastq files that were
corrected by SPades.
I search some of the reads but are unique reads in the files (I'm using
paired end reads)
the only difference that I noticed with the "original" read files is the
following:
Original file:
@HWI-D00173:80:C42H0ACXX:8:1101:1295:2161
CCCCTGTCCACTTCTCTGTGAAAATGAGGGTAATTGACATGATTTCTGTCCCTTTCTATGTGCTTCCATACGTTTATAGAAACCTGTACAGAAG
+
corrected reads file:
@HWI-D00173:80:C42H0ACXX:8:1101:1295:2161
CCCCTGTCCACTTCTCTGTGAAAATGAGGGTAATTGACATGATTTCTGTCCCTTTCTATGTGCTTCCATACGTTTATAGAAACCTGTACAGAAG
+HWI-D00173:80:C42H0ACXX:8:1101:1295:2161
The only difference is that after the "+" spades corrector has copied the
name of the read.
Could be the reason that Mira complains?
Thank you very much,
Vasilis.