[khmer] Dealing with paired-End Data
Alexis Groppi
alexis.groppi at u-bordeaux2.fr
Mon Mar 25 07:29:19 PDT 2013
Hi Titus,
May be a very dumb question :
How to deal with paired-end data (Illumina reads of 75 nt) ?
For some sample, I have paired-end data : it means 2 .fastq file
(SampleN_R1.fastq and SampleN_R2fastq).
What is the best strategy :
a/ Treat each file (R1 and R2) separatly (normalization, filtering,
partition) but then how to deal with the resulting files .part files
from each R1 and R2 for assembly ?
b/ - pooling together these R1 and R2 for each sample
- then perform normalization, filtering, partition and then assembly
considering these data as single end ?
Try to rebuild the pairs in each partition before assembly and then
assembly as paired-end ?
c/strip-and-split-for-assembly ?
d/ Other ?
Thanks for your help
Alexis
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