[mira_talk] Re: Question: padded or unpadded outputs
- From: "abenjak ." <abenjak@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 18 Mar 2015 09:19:50 +0100
BTW, here is a screenshot of a depaded bam derived from a MAF file from
MIRA, visualized in IGV using the original reference (make sure to have an
alias file for IGV because the reference names in the bam files from MIRA
will have the "_bb" suffix).
cheers,
andrej
[image: Inline image 1]
On Wed, Mar 18, 2015 at 9:06 AM, abenjak . <abenjak@xxxxxxxxx> wrote:
> The alignments in the lower half of the screenshot don't match with the
> reference, you see the colored bases?
>
> When you convert from maf to bam, by default the alignments are based on
> the padded reference, so in IGV you must choose the padded sequence as
> reference. You can depad the bam file with samtools depad, but then in
> order to visualize it in IGV, you must provide the unpadded reference. But
> you cannot use the unpadded reference to load padded alignments, or vice
> versa.
>
> The difference between the two alignments (padded bam and unpadded bam)
> will be only on how the insertions are displayed: in the padded version you
> will see what you see in the upper half of your screenshot, in the unpadded
> version there won't be any gap in the reference and the insertions in the
> reads will be displayed in IGV with purple vertical bars (like for the two
> reads in your screenshot, in the 8th position from the right). If you hover
> your mouse over this purple bar, IGV will pop up a balloon with the info
> about the insert for that read.
>
> But the important thing is that both padded or unpadded alignments hold
> the same information. So try to depad your bam and load it in another
> instance of IGV with the unpadded reference and compare the two.
>
> Andrej
>
> On Tue, Mar 17, 2015 at 10:38 PM, lenis vasilis <val1@xxxxxxxxxx> wrote:
>
>> Thank you very much for your support.
>> I'm really sorry for annoying you again but I'm a little bit confused.
>> As I understand (and I'm not so sure about that) the unpadded file is the
>> consensus after the corrections that Mira did into the previous run.
>> I tried to visualize it on igv by converting the maf file into bam.
>> When I'm trying to see the unpadded file it seems that the reads are
>> aligned onto this bases ok
>> How it can be that?
>> Its a little bit confusing the way that Im trying to describe it, so I'm
>> sending you a print screen.
>> The ref genome is the padded file, the first bam is from the padded and
>> the second bam is from the unpadded.
>> The bam file from the padded Fasta has a gap which doesn't exist into the
>> unpadded bam file.
>> Thank you very much, and I'm sorry for the mess again.
>> Vasilis.
>>
>>
>> On Mar 17, 2015, at 8:02 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>
>> wrote:
>>
>> On 17 Mar 2015, at 18:21 , lenis vasilis <val1@xxxxxxxxxx> wrote:
>>
>> In that case, If its possible to have intels, how the unpadded file can
>> be ok?
>>
>>
>> A picture being worth a thousand words, have a look at this;
>>
>> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_intro::srmc_in_454sxahyb_1stpass.png
>>
>> The pads you see in the CONSENSUS line are the ones you see in the padded
>> FASTA file.
>>
>> And I have to agree with Andrej here: you absolutely want to visualise
>> your data in gap4/gap5/Tablet or whatever.
>>
>> B.
>>
>>
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>>
>>
>
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