[mira_talk] Re: SSPACE TAB library information from MIRA caf or maf
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: Robert Willows <robert.willows@xxxxxxxxx>, Andreas Leimbach <andreas.leimbach@xxxxxxxxxxxxxxxx>
- Date: Thu, 13 Feb 2014 16:07:42 +0000
Hi Robert, Andreas, etc.
On 22 Oct 2013, at 23:15 , Robert Willows <robert.willows@xxxxxxxxx> wrote:
> I've been trying to get paired end position and contig information from
> paired end and mate paired libraries in a MIRA assembly to create a
> SSPACE tab file for scaffolding.
>
> ...
It wasn't obvious how to give the tab file to SSPACE from the command
line - I read the Perl code then noticed it was in the manual - the tab file
goes in the library file like this:
Lib1 file1.1.fasta file1.2.fasta 400 0.25 FR
Lib1 file2.1.fasta file2.2.fasta 400 0.25 FR
Lib2 file3.1.fastq file3.2.fastq 4000 0.5 RF
Lib2 TAB file4.tab 4000 0.5 RF
Lib3 TAB file5.tab 10000 0.5 RF
> I realize I can just reuse SSPACE with the original libraries which will map
> the reads with bowtie. I don't want to do this as MIRA has done a much
> better job at placing the reads so I just want to use the position information
> in a tab file for scaffolding.
Also SSPACE v2.0 ignores any reads with N in them before calling bowtie,
and so unlike MIRA it seems to need pre-trimmed FASTQ read files.
On Thu, Oct 24, 2013 at 7:30 AM, Robert Willows
<robert.willows@xxxxxxxxx> wrote:
> Hi all,
>
> Thanks you Bastien and Andreas for pointing me in the right direction,
> I've worked out a protocol for getting the SSPACE tab files from a sam
> file from a MIRA assembly.
>
> Below is the commented protocol using grep and awk.
> ...
Did you try the SSPACE provided tools/sam_bam2Tab.pl script,
http://seqanswers.com/forums/showpost.php?p=68085&postcount=135
(included in SSPACE basic v2.0 at least)?
It seems rather brittle - for instance it assumes for example you've
done single end read mapping so that your SAM/BAM file contains
reads with names ending in /1 and /2 (which shouldn't be there;
the read number *ought* to be in the FLAG field instead and the
read name shouldn't have a suffix at all).
Regards,
Peter
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