Looking for mapper that produces padded alignments

[WhatsOEver]

Hi everyone,
I'm looking for an RNAseq mapping tool (not a de novo assembler!) that is able to output padded alignments ('P' char in the cigar string) against a reference. I would be grateful for any suggestions!
W

[dpryan]

I'd be a bit surprised if one exists. There's no reason to create one to produce padded alignments since padding has no biological meaning. Further, the padding can only be calculated after the mapping is complete, since it's for viewing multiple alignments.

[WhatsOEver]

I know all this... still, I need this kind of alignment. It's just a question whether something like this already exists or I have to write it on my own.

[WhatsOEver]

Maybe it's better to give the example from the sam spec to show what I mean:

Padded alignment.

Most sequence aligners only give the sequences inserted to the reference genome, 
but do not present how these inserted sequences are aligned against each other. 
Alignment with inserted sequences fully aligned is
called padded alignment. Padded alignment is always produced by
de novo assemblers and is important for an alignment viewer to display the 
alignment properly. To store padded alignment, we introduce operation ʻPʼ which 
can be considered as a silent deletion from padded reference sequence. In the 
following example, GA on READ1 and A on READ2 are inserted to the reference. 
With unpadded CIGAR, we would not be able to distinguish the following padded 
multi-alignments:

REF: CACGATCA**GACCGATACGTCCGA           REF: CACGATCA**GACCGATACGTCCGA
READ1: CGATCAGAGACCGATA                  READ1: CGATCAGAGACCGATA
READ2:   ATCA*AGACCGATAC                 READ2:   ATCAA*GACCGATAC
READ3:  GATCA**GACCG                     READ3:  GATCA**GACCG

The padded CIGAR are different:
READ1: 6M2I8M                            READ1: 6M2I8M
READ2: 4M1P1I9M                          READ2: 4M1I1P9M
READ3: 5M2P5M                            READ3: 5M2P5M

I need to work with the left one, not the right one. Are there any tools/libraries/whatever available to do it?

[maubp]

I'm not aware of a tool to do this... You might have to write a bit of code to post-process your traditional alignment output?

[WhatsOEver]

I actually thought there should be something, as these kind of alignments are used in alignment viewers, aren't they?
But there was indeed nothing I could use - I have now written my own code, yes.
I would have closed the thread (or add a "solved" to the title or deleted everything), but that's not possible here, is it?

[maubp]

A few alignment views like 'samtools tview' and bambino can expand inserts, but most SAM/BAM viewers do not show the insert explicitly and ignore CIGAR P operators.

You can edit the title via editing the original post, but this isn't really solved, is it?

[WhatsOEver]

Originally Posted by maubp

A few alignment views like 'samtools tview' and bambino can expand inserts, but most SAM/BAM viewers do not show the insert explicitly and ignore CIGAR P operators.

I looked at bambino and tablet. Both are able to produce padded alignments. But you cannot export them (as no one seems to be interested in it).

You can edit the title via editing the original post

I always use quick editing were you can't edit the title. Have found it under advanced, thanks.

but this isn't really solved, is it?

Well, I couldn't find a tool, nobody could suggest one, I wrote one on my own which works nicely; so, now there is one, which I have. I consider this as solved

[Brian Bushnell]

It's not solved till you make the tool it publicly available

[Matt Kearse]

I'm a little late to this discussion since you've written what you need already. But since your solution isn't publicly available yet I'll point out that Geneious (which is commercial software) has an iterative mapper which produces padded alignments. There is a short video demonstrating this at https://www.youtube.com/watch?v=IOGmxjK3f_4

[WhatsOEver]

@Brian: Good point, but so far its highly tailored to my specific needs. Once it is in a state were someone else can use it, I can make it public.

@Matt: Thanks for the info. I should have mentioned that it is (so far) not important enough to pay for it. I'm actually just testing if this is an improvement to my current project.