SOAP alignment format convert to SAM/BAM

KevinLam · 01-17-2011, 09:28 PM

Dear All,
would you know if there's a convertor for SOAP alignment format to SAM?

gaffa · 01-18-2011, 03:08 AM

There is a script called "soap2sam.pl" - find it here: http://soap.genomics.org.cn/soapaligner.html

Aman Mahajan · 01-23-2012, 12:44 AM

I assembled my illumina data using SOAP, now I want to carry out expression analysis using Rseq tool. it accepts only SAM format so I downloaded SAMTOOLS to convert my soap output to SAM. Can anyone tell me how to run it and convert, tutorial has been of no use yet!

or if you can throw light on how to use this script.

gringer · 01-23-2012, 12:51 AM

From the source code from that script:

Code:

Usage: soap2sam.pl [-p] <aln.soap>

This will output a SAM format file on standard output. If you want that output to be sent to a particular file, then put a redirection sequence ('> aln_file.sam') at the end of the command line.

It looks like the '-p' option is used to indicate that your alignments are paired-end.

Aman Mahajan · 01-23-2012, 01:07 AM

Thanks. but I actually want to know how can I input my file to run through this.

gringer · 01-23-2012, 01:13 AM

Have you aligned your reads using SOAPaligner? That program produces output that can be fed into soap2sam as the 'aln.soap' command-line argument.

Aman Mahajan · 01-23-2012, 02:26 AM

My alignment output has generated a lot of files.. which file out of these has to be the input for soap2sam.pl.. Should the .contig file be renamed as .soap for input?

ganygan25 · 01-23-2012, 03:23 AM

While running soap, the output file name can be explicitly specified.
soap -D <Reference Genome Index> <Read Files> -o <Output File>
(Note:- no file extension required)

This output File can then be converted to SAM format as:-
soap2sam.pl -p <Output File> > <Sam File>.sam

Aman Mahajan · 01-23-2012, 07:33 PM

@ganygany - my output file name is abc.soap.

now I am putting this command

soap2sam.pl abc.soap abc.sam

It generates a sam file but it gives an error message.

gringer · 01-23-2012, 11:47 PM

you missed out the > symbol

Aman Mahajan · 01-24-2012, 12:07 AM

I have put this symbol now

soap2sam.pl abc.soap > abc.sam..

Error of command not found. If i put this command :-

perl soap2sam.pl abc.soap > abc.sam..

Still the same result, file generated of the name abc.soap but zero space..

ganygan25 · 01-24-2012, 12:24 AM

"Error of command not found. "
Not a soap issue. Could your verify your installation and run them again?
Or post your sequence of commands here..

"file generated of the name abc.soap but zero space"
If your commands are fine, do you mean to say that there are no reads aligned ??

Aman Mahajan · 01-24-2012, 12:29 AM

Okay. I aligned my data using SOAP so I have a file abc.soap which is aligned.

I have copied this file in the same folder with soap2sam.pl. Now I am trying to run soap2sam.pl on this file abc.soap.

My command is not showing any error but the output generated i.e abc.sam is of zero space.

Any idea if there is a need to compile soap2sam.pl first because I am using it through samtools.

Thank you.

gringer · 01-24-2012, 12:35 AM

could you please show the result of running the following command (including the exact error, if any)? I suspect that soap2sam isn't in the directory that you're trying to run it from.

Code:

ls $(pwd)/soap2sam.pl $(pwd)/abc.soap

Aman Mahajan · 01-24-2012, 12:41 AM

result is

/root/Desktop/samtools-0.1.18/misc/soap2sam.pl

in the same folder i have my file abc.soap

gringer · 01-24-2012, 12:46 AM

Okay, but you shouldn't really be running that as root. Anyway, another command to try:

Code:

pwd && perl ./soap2sam.pl

If that works (and shows the help/usage message), then this one should also work:

Code:

perl ./soap2sam.pl abc.soap > abc.sam

gringer · 01-24-2012, 12:56 AM

no such file or directory for what? could you please copy the exact error?

Aman Mahajan · 01-24-2012, 12:57 AM

Sorry I typed the wrong file name. corrected it and ran it..the command runs and generates an output but same zero space it has..

Aman Mahajan · 01-24-2012, 01:02 AM

I mean I typed it as ab.soap by mistake. Corrected it and ran again. but the output file is again empty.

gringer · 01-24-2012, 01:02 AM

Have you checked the input file to see if it looks right?

Code:

head abc.soap

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01-17-2011, 09:28 PM	#1
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 197	SOAP alignment format convert to SAM/BAM Dear All, would you know if there's a convertor for SOAP alignment format to SAM?

01-23-2012, 12:51 AM	#4
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 823	From the source code from that script: Code: Usage: soap2sam.pl [-p] <aln.soap> This will output a SAM format file on standard output. If you want that output to be sent to a particular file, then put a redirection sequence ('> aln_file.sam') at the end of the command line. It looks like the '-p' option is used to indicate that your alignments are paired-end.

01-24-2012, 12:35 AM	#14
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 823	could you please show the result of running the following command (including the exact error, if any)? I suspect that soap2sam isn't in the directory that you're trying to run it from. Code: ls $(pwd)/soap2sam.pl $(pwd)/abc.soap

01-24-2012, 12:46 AM	#16
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 823	Okay, but you shouldn't really be running that as root. Anyway, another command to try: Code: pwd && perl ./soap2sam.pl If that works (and shows the help/usage message), then this one should also work: Code: perl ./soap2sam.pl abc.soap > abc.sam

01-18-2011, 03:08 AM	#2
gaffa Member Location: Gothenburg/Uppsala, Sweden Join Date: Oct 2010 Posts: 82	There is a script called "soap2sam.pl" - find it here: http://soap.genomics.org.cn/soapaligner.html

01-23-2012, 12:44 AM	#3
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	I assembled my illumina data using SOAP, now I want to carry out expression analysis using Rseq tool. it accepts only SAM format so I downloaded SAMTOOLS to convert my soap output to SAM. Can anyone tell me how to run it and convert, tutorial has been of no use yet! or if you can throw light on how to use this script.

01-23-2012, 01:07 AM	#5
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	Thanks. but I actually want to know how can I input my file to run through this.

01-23-2012, 01:13 AM	#6
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 823	Have you aligned your reads using SOAPaligner? That program produces output that can be fed into soap2sam as the 'aln.soap' command-line argument.

01-23-2012, 02:26 AM	#7
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	My alignment output has generated a lot of files.. which file out of these has to be the input for soap2sam.pl.. Should the .contig file be renamed as .soap for input?

01-23-2012, 03:23 AM	#8
ganygan25 Junior Member Location: UK Join Date: Dec 2011 Posts: 9	While running soap, the output file name can be explicitly specified. soap -D <Reference Genome Index> <Read Files> -o <Output File> (Note:- no file extension required) This output File can then be converted to SAM format as:- soap2sam.pl -p <Output File> > <Sam File>.sam

01-23-2012, 07:33 PM	#9
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	@ganygany - my output file name is abc.soap. now I am putting this command soap2sam.pl abc.soap abc.sam It generates a sam file but it gives an error message.

01-23-2012, 11:47 PM	#10
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 823	you missed out the > symbol

01-24-2012, 12:07 AM	#11
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	I have put this symbol now soap2sam.pl abc.soap > abc.sam.. Error of command not found. If i put this command :- perl soap2sam.pl abc.soap > abc.sam.. Still the same result, file generated of the name abc.soap but zero space..

01-24-2012, 12:24 AM	#12
ganygan25 Junior Member Location: UK Join Date: Dec 2011 Posts: 9	"Error of command not found. " Not a soap issue. Could your verify your installation and run them again? Or post your sequence of commands here.. "file generated of the name abc.soap but zero space" If your commands are fine, do you mean to say that there are no reads aligned ??

01-24-2012, 12:29 AM	#13
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	Okay. I aligned my data using SOAP so I have a file abc.soap which is aligned. I have copied this file in the same folder with soap2sam.pl. Now I am trying to run soap2sam.pl on this file abc.soap. My command is not showing any error but the output generated i.e abc.sam is of zero space. Any idea if there is a need to compile soap2sam.pl first because I am using it through samtools. Thank you.

01-24-2012, 12:41 AM	#15
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	result is /root/Desktop/samtools-0.1.18/misc/soap2sam.pl in the same folder i have my file abc.soap

01-24-2012, 12:56 AM	#17
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 823	no such file or directory for what? could you please copy the exact error?

01-24-2012, 12:57 AM	#18
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	Sorry I typed the wrong file name. corrected it and ran it..the command runs and generates an output but same zero space it has..

01-24-2012, 01:02 AM	#19
Aman Mahajan Member Location: India Join Date: Jan 2012 Posts: 22	I mean I typed it as ab.soap by mistake. Corrected it and ran again. but the output file is again empty.