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Old 04-20-2011, 11:14 AM   #2
jvhaarst
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Location: Netherlands

Join Date: Sep 2008
Posts: 13
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It has been a while since I looked at SOAPdenovo, but could you try this config ?
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#maximal read length
max_rd_len=100
[LIB]
#average insert size
avg_ins=200
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=1
#in which order the reads are used while scaffolding
rank=1
q=/common/groups/Illx/Unpaired_SIPES_PF_lane5_1_trimmed.fastq
q1=/common/groups/Illx/Unpaired_SIPES_PF_lane7_1_trimmed.fastq

[LIB]
#average insert size
avg_ins=200
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#in which order the reads are used while scaffolding
rank=2
q=/common/groups/Illx/Genomic_SIPES_lane5_1_paired_trimmed_paired.fastq
q1=/common/groups/Illx/Genomic_SIPES_lane6_1_paired_trimmed_paired.fastq
q2=/common/groups/Illx/Genomic_SIPES_lane7_1_paired_trimmed_paired.fastq
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