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Old 01-31-2008, 07:22 AM   #1
ECO
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Default SOAP: short oligonucleotide alignment program.

New paper out describing a new alignment tool. I don't have a subscription to Bioinformatics, so I must be content with the abstract until I can dig up the paper...

Quote:
MOTIVATION: We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery, and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multithreaded parallel computing, and has a batch module for multiple query sets. AVAILABILITY: http://soap.genomics.org.cn CONTACT: [email protected].
http://www.ncbi.nlm.nih.gov/pubmed/18227114

edit: Due to intermittent downtime of the original SOAP site above, I've hosted the current tar file as an attachment here. If the author has any problem with this please let me know.
Attached Files
File Type: gz soap_1.10.tar.gz (49.4 KB, 11 views)
File Type: gz soap_1.11.tar.gz (49.0 KB, 4 views)
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Old 05-03-2008, 07:45 AM   #2
RudyS
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Default cant find SOAP site in canada

this program is supposed to be available at

http://soap.genomics.org.cn

but cant access the site

i was handed a file for a resequencing project for a microcystis strain that doesnt produce toxins ... i dont have the solexa software ... i ran a program called rmap using a fasta version i created of the solexa file against the published m.aer 6megbase genome and the sequences look promising ... so how do people who dont have the solexa software align their sequences? i have 5,130,912 sequences of 36 bases each ... rmap identifies about 120,000 of them as having nomismatches with the published genome ... about 360,000 have 1 or none mismatches ... the rmap output has start and stop positions and an indicator of the strand ...

i am thinking it would be easier to do this with a program like SOAP if it were publicly available ... ?

any suggestions ?

thanks a bunch in advance

rudy
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Old 05-03-2008, 08:22 AM   #3
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hey rudy. welcome. definitely sounds like you need to take a look at this thread:

http://seqanswers.com/forums/showthread.php?t=43

...and the SOAP site is down for me too... :/
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Old 05-03-2008, 09:13 AM   #4
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Default yuchang ::AT:: genomics.org.cn

ECO

kind fellow in canada sent me a tar file with the SOAP software with apologies for inconvenience accessing site ... will let you know what i find ... thanks for list of links
rudy
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Old 05-05-2008, 01:28 PM   #5
myrna
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Default SOAP site down, still

It is disappointing when a paper comes out and the download site for the software doesn't even last a month. If anyone on this board has the SOAP package, could they post a mirror (or send it to me)?

Thanks,

Ryan
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Old 05-05-2008, 02:01 PM   #6
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Quote:
Originally Posted by myrna View Post
It is disappointing when a paper comes out and the download site for the software doesn't even last a month. If anyone on this board has the SOAP package, could they post a mirror (or send it to me)?

Thanks,

Ryan
As usual, if someone PM's me, I will host it!
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Old 05-06-2008, 05:24 AM   #7
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Default SOAP site is back up

The SOAP site is available again

Tim
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Old 05-06-2008, 07:15 AM   #8
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It's back up for me too, but I've hosted the tar in the first post just in case! Thanks RudyS.
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Old 07-06-2008, 09:25 AM   #9
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Any hints on compiling this thing on OSX?

Code:
[email protected]##:~/perl/soap/soap_1.10$ sudo make
Password:
g++ -static -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c align.cpp -o align.chr.o
/var/tmp//ccrPoVlo.s:20045:FATAL:incompatible feature used: section type non_lazy_symbol_pointers (must specify "-dynamic" to be used)
make: *** [align.chr.o] Error 1
[email protected]##:~/perl/soap/soap_1.10$
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Old 07-14-2008, 08:10 AM   #10
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Quote:
Originally Posted by ECO View Post
Any hints on compiling this thing on OSX?

Code:
[email protected]##:~/perl/soap/soap_1.10$ sudo make
Password:
g++ -static -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c align.cpp -o align.chr.o
/var/tmp//ccrPoVlo.s:20045:FATAL:incompatible feature used: section type non_lazy_symbol_pointers (must specify "-dynamic" to be used)
make: *** [align.chr.o] Error 1
[email protected]##:~/perl/soap/soap_1.10$
You can remove "-static" from the FLAGS= line in the makefile
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Old 07-15-2008, 08:19 AM   #11
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Quote:
Originally Posted by jjcook View Post
You can remove "-static" from the FLAGS= line in the makefile
Thanks JJcook...that worked a treat. I have another problem with this one, this time on openSUSE11:

Code:
ericbox:/home/eco/dl/soap_1.10 # make
g++ -static -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c main.cpp -o main.chr.o
In file included from main.cpp:11:
align.h: In member function ‘void SingleAlign::Reverse_Seq()’:
align.h:286: error: ‘reverse’ was not declared in this scope
align.h: In member function ‘void SingleAlign::Reverse_Qual()’:
align.h:294: error: ‘reverse’ was not declared in this scope
main.cpp: In function ‘void usage()’:
main.cpp:294: error: ‘exit’ was not declared in this scope
main.cpp: In function ‘int mGetOptions(int, char**)’:
main.cpp:308: error: ‘atoi’ was not declared in this scope
main.cpp: In function ‘void RunProcess()’:
main.cpp:348: error: ‘exit’ was not declared in this scope
main.cpp:353: error: ‘exit’ was not declared in this scope
main.cpp:358: error: ‘exit’ was not declared in this scope
main.cpp:363: error: ‘exit’ was not declared in this scope
main.cpp:385: error: ‘exit’ was not declared in this scope
main.cpp:391: error: ‘exit’ was not declared in this scope
main.cpp:398: error: ‘exit’ was not declared in this scope
main.cpp: In function ‘int main(int, char**)’:
main.cpp:428: error: ‘exit’ was not declared in this scope
make: *** [main.chr.o] Error 1

Last edited by ECO; 07-15-2008 at 09:05 PM. Reason: to follow up on the OSX change working...
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Old 07-15-2008, 10:09 AM   #12
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In align.h, you may need to change the 'reverse' call to 'std::reverse'

In main.cpp, you should add
Code:
#include <stdlib.h>
to the top of the file.

Given I can't duplicate your error with my version of gcc, I can't test if those fixes will work -- but hopefully they do
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Old 07-15-2008, 12:17 PM   #13
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Quote:
Originally Posted by jjcook View Post
In align.h, you may need to change the 'reverse' call to 'std::reverse'

In main.cpp, you should add
Code:
#include <stdlib.h>
to the top of the file.

Given I can't duplicate your error with my version of gcc, I can't test if those fixes will work -- but hopefully they do
We're gettin' there...thanks again for your help. The #include removed most of the errors:

Code:
g++ -static -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c main.cpp -o main.chr.o
In file included from main.cpp:12:
align.h: In member function ‘void SingleAlign::Reverse_Seq()’:
align.h:286: error: ‘reverse’ was not declared in this scope
align.h: In member function ‘void SingleAlign::Reverse_Qual()’:
align.h:294: error: ‘reverse’ was not declared in this scope
make: *** [main.chr.o] Error 1
...then changing the align.h didn't appear to work...

Code:
g++ -static -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c main.cpp -o main.chr.o
In file included from main.cpp:12:
align.h: In member function ‘void SingleAlign::Reverse_Seq()’:
align.h:286: error: ‘reverse’ is not a member of ‘std’
align.h: In member function ‘void SingleAlign::Reverse_Qual()’:
align.h:294: error: ‘reverse’ is not a member of ‘std’
make: *** [main.chr.o] Error 1
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Old 07-15-2008, 12:21 PM   #14
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Ah -- you need to add this to align.h:

Code:
#include<algorithm>
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Old 07-15-2008, 01:59 PM   #15
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Heh...error keeps getting shorter....I also removed the -static flag on advice received from the SOAP team.

Code:
g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c main.cpp -o main.chr.o
g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c pairs.cpp -o pairs.chr.o
g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c param.cpp -o param.chr.o
param.cpp: In member function ‘void Param::SetMrnaTag(int)’:
param.cpp:98: error: ‘exit’ was not declared in this scope
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Old 07-15-2008, 06:54 PM   #16
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Place this near the top of param.cpp:

Code:
#include<stdlib.h>
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Old 07-16-2008, 09:08 AM   #17
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No luck...I'm corresponding with the SOAP team, hopefully they will be able to help me through it. Thanks for the help jjcook

Code:
g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c param.cpp -o param.chr.o
g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c reads.cpp -o reads.chr.o
reads.cpp: In member function ‘void ReadClass::CheckFile(std::ifstream&)’:
reads.cpp:32: error: ‘exit’ was not declared in this scope
reads.cpp:37: error: ‘exit’ was not declared in this scope
reads.cpp:41: error: ‘exit’ was not declared in this scope
make: *** [reads.chr.o] Error 1
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Old 07-17-2008, 11:55 PM   #18
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New version out today... see:

ftp://ftp.genomics.org.cn/pub/soap/
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Old 07-18-2008, 08:21 AM   #19
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1.11 has solved all my compiling problems. Now to find some indels!
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Old 07-14-2009, 01:40 PM   #20
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Any luck with soap on indels?
I tried it on my paired-end data, but soapsnp ends up in segmentation fault!
I think I did fine on the sort (confused about sorting a paired end alignment on coordinates!) .. does soap not use the information of pairs after mapping them!
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