SOAP alignment format convert to SAM/BAM

[KevinLam]

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

[gaffa]

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

[Aman Mahajan]

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]

From the source code from that script:

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]

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

[gringer]

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]

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]

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]

@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]

you missed out the > symbol

[Aman Mahajan]

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]

"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]

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]

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.

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

[Aman Mahajan]

result is


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


in the same folder i have my file abc.soap