SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SOAPdenovo v1.05 scami Bioinformatics 1 01-05-2013 12:04 AM
SOAPdenovo -error robelb4 Bioinformatics 0 08-05-2011 12:39 PM
error from SOAPdenovo shuang Bioinformatics 6 07-15-2011 08:43 AM
issues with SOAPdenovo bioBob Bioinformatics 2 04-20-2011 01:17 PM
SOAPdenovo AnthonyB Bioinformatics 2 05-30-2009 07:12 PM

Reply
 
Thread Tools
Old 08-12-2009, 06:12 AM   #1
vani s kulkarni
Member
 
Location: Netherlands

Join Date: Jun 2009
Posts: 11
Default 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..
vani s kulkarni is offline   Reply With Quote
Old 08-12-2009, 09:01 AM   #2
geschickten
Member
 
Location: India

Join Date: Jul 2009
Posts: 31
Default

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
geschickten is offline   Reply With Quote
Old 08-12-2009, 11:26 PM   #3
strob
Member
 
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default

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.
strob is offline   Reply With Quote
Old 08-13-2009, 02:51 AM   #4
BENM
Member
 
Location: PRC

Join Date: May 2009
Posts: 33
Default

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
BENM is offline   Reply With Quote
Old 06-14-2013, 11:53 AM   #5
osha84
Junior Member
 
Location: NYC

Join Date: May 2013
Posts: 7
Default

I also did the same but it keeps giving me [LIB] command not found error. does anyone know how to solve this problem please.
osha84 is offline   Reply With Quote
Old 06-17-2013, 12:08 AM   #6
Linnea
Member
 
Location: Uppsala, Sweden

Join Date: Mar 2010
Posts: 23
Default

Quote:
Originally Posted by osha84 View Post
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?
Linnea is offline   Reply With Quote
Old 06-17-2013, 01:08 PM   #7
osha84
Junior Member
 
Location: NYC

Join Date: May 2013
Posts: 7
Default

Quote:
Originally Posted by Linnea View Post
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.
osha84 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:29 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO