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Thread | Thread Starter | Forum | Replies | Last Post |
How to convert BED format to SAM/BAM? | seq_newbie | Bioinformatics | 1 | 06-23-2011 08:11 AM |
Looking process to convert gff3 format into ace format or sam format | andylai | Bioinformatics | 1 | 05-17-2011 02:09 AM |
how to convert from bam or sam to map | rcorbett | Bioinformatics | 1 | 11-04-2010 10:49 AM |
convert BAM -> SAM? | thinkRNA | Bioinformatics | 4 | 06-30-2010 03:08 AM |
Convert MAQ,SOAP alignment result to ACE format | baohua100 | Bioinformatics | 0 | 03-02-2009 01:01 AM |
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#1 |
Senior Member
Location: SEA Join Date: Nov 2009
Posts: 197
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Dear All,
would you know if there's a convertor for SOAP alignment format to SAM? |
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#2 |
Member
Location: Gothenburg/Uppsala, Sweden Join Date: Oct 2010
Posts: 82
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There is a script called "soap2sam.pl" - find it here: http://soap.genomics.org.cn/soapaligner.html
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#3 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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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. |
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#4 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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From the source code from that script:
Code:
Usage: soap2sam.pl [-p] <aln.soap> It looks like the '-p' option is used to indicate that your alignments are paired-end. |
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#5 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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Thanks. but I actually want to know how can I input my file to run through this.
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#6 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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Have you aligned your reads using SOAPaligner? That program produces output that can be fed into soap2sam as the 'aln.soap' command-line argument.
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#7 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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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?
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#8 |
Junior Member
Location: UK Join Date: Dec 2011
Posts: 9
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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 |
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#9 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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@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. |
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#10 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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you missed out the > symbol
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#11 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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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.. |
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#12 |
Junior Member
Location: UK Join Date: Dec 2011
Posts: 9
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"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 ?? |
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#13 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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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. |
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#14 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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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 |
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#15 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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result is
/root/Desktop/samtools-0.1.18/misc/soap2sam.pl in the same folder i have my file abc.soap |
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#16 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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Okay, but you shouldn't really be running that as root. Anyway, another command to try:
Code:
pwd && perl ./soap2sam.pl Code:
perl ./soap2sam.pl abc.soap > abc.sam |
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#17 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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no such file or directory for what? could you please copy the exact error?
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#18 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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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..
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#19 |
Member
Location: India Join Date: Jan 2012
Posts: 22
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I mean I typed it as ab.soap by mistake. Corrected it and ran again. but the output file is again empty.
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#20 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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Have you checked the input file to see if it looks right?
Code:
head abc.soap |
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