Hello,
I tried an assembly with paired and and mate pairs:
mpiexec -n 32 Ray \
-k \
89 \
-p \
/shared/reads/GDR-16_R1.NoAdaptPR.fastq \
/shared/reads/GDR-16_R2.NoAdaptPR.fastq \
283 \
20 \
-p \
GDR17_NoPseudomonas_R1_RC.fastq \
GDR17_NoPseudomonas_R2_RC.fastq \
2397 \
649 \
-o \
Miseq_MP_k89
The MiSeq paired end are 250bp each, so they overlap a lot since the
fragment is 283. The Mate pairs however are 100bp, and are likely
contaminated with paired end. I supplied this command, and the assembly did
not return very good stats.
Should I maybe try the Mate Pairs without a predefined distance, and see
what Ray estimates the fragment size to be?
Is there any way to find out what the problem is? I know that by doing an
assembly on just the MiSeq with high kmers (above 200) I get better stats.
Adrian
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