[mira_talk] Re: SSPACE TAB library information from MIRA caf or maf
- From: Robert Willows <robert.willows@xxxxxxxxx>
- To: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- Date: Fri, 14 Feb 2014 12:51:57 +1100
On 14 Feb 2014, at 12:33 pm, Robert Willows <robert.willows@xxxxxxxxx> wrote:
> Hi Peter,
>
> I've attached a shell script for making the TAB files from the miraconvert
> produced sam file which has been depadded (instructions for depadding are
> given in the script). The script tries to make 5 libraries and tells you
> which ones have paired reads in them.
>
> Also, I just found a problem in the sam file produced in the version 4.0 of
> miraconvert when making the sam file from the maf. So you need to use
> miraconvert from version 4.0rc4 (release candidate #4) to make the sam file
> which makes the sam file correctly. I'll post a new thread about this.
Oops. My mistake 4.0 and 4.0rc4 sam files are both OK.
Sorry.
>
> Regards
> Robert
> <SAM-SSPACE-OUT.sh>
>
>
>
> On 14 Feb 2014, at 3:07 am, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
>
>> 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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