[gringer]

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

pwd && perl ./soap2sam.pl

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

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

[gringer]

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

[Aman Mahajan]

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]

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

[gringer]

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

head abc.soap

[Aman Mahajan]

Yes. the command "head" works . shows me the initial contents of the file.

[gringer]

shows me the initial contents of the file

And what are these contents? Could you please show the output?

This page suggests it should be a 9-column output, tab separated:

http://soap.genomics.org.cn/soap1/#Formatofoutput

To confirm tab separated, you can do this:

hexdump -C abc.soap | head

and look for '09' between fields in the left hand side of the output.

[Aman Mahajan]

>3 length 34 cvg_0.0_tip_0
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT
>5 length 34 cvg_0.0_tip_0
AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

These are the first intial lines of the file abc.soap.


On running the command you mentioned, I get an output , not sure what you mentioned to look for means.

[gringer]

>3 length 34 cvg_0.0_tip_0
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT
>5 length 34 cvg_0.0_tip_0
AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

That's a FASTA file, not a SOAP alignment file. Are you sure you ran SOAP (i.e. the SOAPaligner program) rather than SOAPdenovo to get this output?

[Aman Mahajan]

We ran soapdenovo on this...so we have to use soapaligner ??

I mean the output isn't same for soapdenovo and soapaligner??..

And lastly if I have to convert only this fasta file into SAM, what should I do?..is it possible?

[gringer]

We ran soapdenovo on this...so we have to use soapaligner ??
I mean the output isn't same for soapdenovo and soapaligner??

Assembly and alignment are two different things. soap2sam.pl expects alignments in the format produced by SOAP (i.e. SOAPaligner). If you don't want to use SOAP for this, there are plenty of other programs for mapping that can produce SAM files directly as output.

And lastly if I have to convert only this fasta file into SAM, what should I do?..is it possible?

You may be able to simulate reads using the coverage values in the sequence headers, but that would be silly because it wouldn't be a true representation of your data. Also, you would still need to work out a way to generate SAM files.

[Aman Mahajan]

Sorry to bother you, I am naive in this field.

Actually I did not use SOAPaligner as it requires a reference to run I think. So I used Soapdenovo. Now I want to run this output in Rseq for quantification of my data.

But Rseq requires SAM format as input so i have been trying to convert it to SAM.

Which softwares I must use , if you can suggest?

[Aman Mahajan]

And I want to user mrfQuantifier in Rseq, so basically I need the SAM format as input for it or is there anyway to convert it to MRF directly without involving a SAM conversion step.

[arvid]

Maybe you should read up on assembly, alignment and quantification before messing around too much with the different software...

The contigs generated by SOAPdenovo can be used as a reference for quantification. You can align the reads to those contigs with e.g. SOAPaligner to get a file with aligned reads (in the SOAP format) that you can convert into SAM for further analysis. Or you can use a software like RSEM for quantification.

[arvid]

Also you should possibly try a transcriptome-centric assembler such as Trinity, Trans-ABySS, Oases or SOAPdenovo-Trans instead of SOAPdenovo, which is optimized for genomic assembly.