SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   SOAP: short oligonucleotide alignment program. (http://seqanswers.com/forums/showthread.php?t=49)

ECO 01-31-2008 07:22 AM

SOAP: short oligonucleotide alignment program.
 
2 Attachment(s)
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: soap@genomics.org.cn.
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.

RudyS 05-03-2008 07:45 AM

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

ECO 05-03-2008 08:22 AM

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... :/

RudyS 05-03-2008 09:13 AM

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

myrna 05-05-2008 01:28 PM

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

ECO 05-05-2008 02:01 PM

Quote:

Originally Posted by myrna (Post 538)
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! :D

tab 05-06-2008 05:24 AM

SOAP site is back up
 
The SOAP site is available again

Tim

ECO 05-06-2008 07:15 AM

It's back up for me too, but I've hosted the tar in the first post just in case! Thanks RudyS.

ECO 07-06-2008 09:25 AM

Any hints on compiling this thing on OSX?

Code:

eco@##:~/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
eco@##:~/perl/soap/soap_1.10$


jjcook 07-14-2008 08:10 AM

Quote:

Originally Posted by ECO (Post 928)
Any hints on compiling this thing on OSX?

Code:

eco@##:~/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
eco@##:~/perl/soap/soap_1.10$


You can remove "-static" from the FLAGS= line in the makefile

ECO 07-15-2008 08:19 AM

Quote:

Originally Posted by jjcook (Post 1004)
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


jjcook 07-15-2008 10:09 AM

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 :)

ECO 07-15-2008 12:17 PM

Quote:

Originally Posted by jjcook (Post 1022)
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


jjcook 07-15-2008 12:21 PM

Ah -- you need to add this to align.h:

Code:

#include<algorithm>

ECO 07-15-2008 01:59 PM

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


jjcook 07-15-2008 06:54 PM

Place this near the top of param.cpp:

Code:

#include<stdlib.h>

ECO 07-16-2008 09:08 AM

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


ECO 07-17-2008 11:55 PM

New version out today... see:

ftp://ftp.genomics.org.cn/pub/soap/

ECO 07-18-2008 08:21 AM

1.11 has solved all my compiling problems. Now to find some indels! :D

bioinfosm 07-14-2009 01:40 PM

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!


All times are GMT -8. The time now is 07:08 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.