[mira_talk] Re: Problem with convert_project
- From: Steven Sijmons <steven.sijmons@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 29 Oct 2012 05:04:58 +0100
Thanks for the advice. I was indeed using MIRA 3.4.0.1. I guess making the
switch to the newest version would make most sense, should have done that
already actually. I'll get in touch if I still encounter problems, but this
should probably solve the issue. Anyway, thanks for your time!
Best regards,
Steven
2012/10/28 Bastien Chevreux <bach@xxxxxxxxxxxx>
> On 10/26/2012 09:14 PM, Steven Sijmons wrote:
>
>> [...]
>>
>> When I then compared the number of reads in the fastq file I created with
>> convert_project, I noticed that these contained more reads than the number
>> of lines present in the debris_list. Debris_lists contained 232 628, 2 288
>> 887 and 42 826 127 reads, while the convert_project outputs contained 437
>> 106, 2 392 084 and 43 632 082 reads respectively. Could these 'extra' reads
>> be causing this? And where are these reads coming from if they aren't in
>> the debris_list? Hoping that someone can give some possible explanations
>> for this, because I really don't understand what's happening here.
>>
>
> Thanks for the data. Am I correct in guessing you used MIRA 3.4.x? Well,
> I'm quite sure of it actually.
>
> Two things play a role in this misbehaviour you are seeing:
> - MIRA 3.4.x does not recognise CASAVA 1.8 style Illumina paired-end data.
> One needs to rename reads before 3.4.x sees that they are paired end. You
> did not do that.
> This naming convention problem also applies to convert_project from the
> same package.
> - MIRA 3.4.x has a broken "check for doubly appearing reads" routine ...
> it does not recognise when two reads with the same name are given. This
> happens with CASAVA 1.8 style naming.
>
> Possible fixes are simple, but you will need to redo assemblies:
>
> 1) if you want to continue with MIRA 3.4.x, you need to rename Illumina
> reads from CASAVA pipelines >= 1.8. That is, if a FASTQ definition is
> @somename 1:whatever
> you need to rename it to
> @somename/1 1:whatever
> and similarly for the other half of the pair ("2" instead of "1" above)
>
> 2) You switch to MIRA 3.9.x and the naming problems are automatically
> solved
>
> Hope that helps,
> Bastien
>
>
>
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