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Old 04-20-2011, 09:33 AM   #1
bioBob
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Location: Virginia

Join Date: Mar 2011
Posts: 72
Default issues with SOAPdenovo

Hello.
I am wondering if anyone here some some experience with SOAPdenovo.

I am trying to assembly Illumina data, I have 3 lanes of 101 cycle PE data and 2 lanes of single read data.

I have tried all sorts of options for running the program down to the default ./SOAPdenovo63mer all -s SOAPdenovo_config.txt -o out_

At the end of the day (ok, only 2 hours), it is telling me 'no paired reads found' and tossed a terminal error.

I have used this same data in both CLC and Velvet and it works fine including scaffolding in Velvet and paired mapping in CLC.

I am sure I am doing something silly. Any thoughts?

Thanks,
Bob

ps. my config file is:

#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
p=/common/groups/Illx/Genomic_SIPES_lane5_1_paired_trimmed_paired.fastq
p=/common/groups/Illx/Genomic_SIPES_lane6_1_paired_trimmed_paired.fastq
p=/common/groups/Illx/Genomic_SIPES_lane7_1_paired_trimmed_paired.fastq
q=/common/groups/Illx/Unpaired_SIPES_PF_lane5_1_trimmed.fastq
q=/common/groups/Illx/Unpaired_SIPES_PF_lane7_1_trimmed.fastq
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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
Default

It has been a while since I looked at SOAPdenovo, but could you try this config ?
----
#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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Old 04-20-2011, 12:17 PM   #3
bioBob
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Location: Virginia

Join Date: Mar 2011
Posts: 72
Default

Thanks.

Unfortunately, it appears as though it was a case of RTFM more carefully. Paired reads have to be in fast-a format if in a single file. I only wasted 2 days because I didn't see that earlier. =/
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