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-   -   SOAPdenovo (http://seqanswers.com/forums/showthread.php?t=2304)

vani s kulkarni 08-12-2009 06:12 AM

SOAPdenovo
 
Hi

I want to use SOAPdenovo assembler for my solexa short reads.
But am not understanding what is Configuration file and how can I do that? Can any one explain me this Configuration file and help me to start.


thanks..

geschickten 08-12-2009 09:01 AM

Vani,

If you think you can share your data with then I can help you. Let me know your requirements. You can reach me at prahalad@geschickten.com

strob 08-12-2009 11:26 PM

Hi,

I has similar questions so I just mailed the people from SOAP (look for email at their website). I got quick answers and they helped me to optimize my parameters!!

Really helpful.

BENM 08-13-2009 02:51 AM

APPENDIX: example.config
#maximal read length
max_rd_len=50
[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=1
#fastq file for read 1
q1=/path/**LIBNAMEA**/fastq_read_1.fq
#fastq file for read 2 always follows fastq file for read 1
q2=/path/**LIBNAMEA**/fastq_read_2.fq
#fasta file for read 1
f1=/path/**LIBNAMEA**/fasta_read_1.fa
#fastq file for read 2 always follows fastq file for read 1
f2=/path/**LIBNAMEA**/fasta_read_2.fa
#fastq file for single reads
q=/path/**LIBNAMEA**/fastq_read_single.fq
#fasta file for single reads
f=/path/**LIBNAMEA**/fasta_read_single.fa
#a single fasta file for paired reads
p=/path/**LIBNAMEA**/pairs_in_one_file.fa
[LIB]
avg_ins=2000
reverse_seq=1
asm_flags=2
rank=2
q1=/path/**LIBNAMEB**/fastq_read_1.fq
q2=/path/**LIBNAMEB**/fastq_read_2.fq
q=/path/**LIBNAMEB**/fastq_read_single.fq
f=/path/**LIBNAMEB**/fasta_read_single.fa

osha84 06-14-2013 11:53 AM

I also did the same but it keeps giving me [LIB] command not found error. does anyone know how to solve this problem please.

Linnea 06-17-2013 12:08 AM

Quote:

Originally Posted by osha84 (Post 107675)
I also did the same but it keeps giving me [LIB] command not found error. does anyone know how to solve this problem please.

Did you get "[LIB] command" not found? First I read "[LIB] not found" and interpreted it as SOAP didn't find the fastq file - I had that problem and it helped when I added the full path instead of "~"-annotation (changing ~/soap/file.fastq to /home/linnea/soap/file.fastq).
The format of the config file is quite strict, for example you are not allowed to have any extra blank lines in the end.

But if it says command not found it sounds like it's trying to run the config file or something.. What command did you use for starting SOAP?

osha84 06-17-2013 01:08 PM

Quote:

Originally Posted by Linnea (Post 107776)
Did you get "[LIB] command" not found? First I read "[LIB] not found" and interpreted it as SOAP didn't find the fastq file - I had that problem and it helped when I added the full path instead of "~"-annotation (changing ~/soap/file.fastq to /home/linnea/soap/file.fastq).
The format of the config file is quite strict, for example you are not allowed to have any extra blank lines in the end.

But if it says command not found it sounds like it's trying to run the config file or something.. What command did you use for starting SOAP?

Hi Lennea,
It actually said [LIB] not found. I used my mackbook to install the tools and it didn't work until I realized that it doesn't wrok on mac so I had to install Parallels so I can run Windows applications in my Mac. Problem was solved and I'm enjoying working on Parallels.


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