CAGE tags

[LukaszKielpinski]

Hi Everybody!

My problem is about mapping where only the location of 5'end of the read is meaningful, rest of the sequence is needed only to direct this end into the location - let's call this location a CAGE tag.
I did mapping using TopHat and while it is very easy to extract CAGE tags for +strand (it is read start position in SAM file), it is not at all the same story for minus strand. If this were bowtie mapping I would just add read length to the start position, but since this mapping allows for indels and exons it is always different number that would have to been added (it is possible to deduce it from CIGAR).
Do any of you know a straightforward method of obtaining this CAGE tags, or I have to figure out how to use CIGAR?
Best,
Lukasz

Edit: After more extensive search I found that in R package GenomicRanges there is function cigarToWidth() which is what I need! Anyway, maybe there are some even easier solutions.

[Dario1984]

Why did you use TopHat ? CAGE tags are short. It doesn't work well with reads less than about 50 bases long.

[LukaszKielpinski]

It is actually not exactly CAGE protocol, this is only "CAGE-like" mapping philosophy where only interesting information is the 5'end location. My reads are 94 nt.

[SEQond]

CAGE pipeline software

Why did you use TopHat ? CAGE tags are short. It doesn't work well with reads less than about 50 bases long.

Dario1984 do you use as a pipeline the exact software mentioned in the article 1. Takahashi, H., et al., 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc, 2012. 7(3): p. 542-61.

?

Since I haven't found any thing else this is what I use.

[Dario1984]

That's a good reference. I need to read it in detail. They use BWA to do mapping. I would agree with that. We use Bowtie, which is similar. TopHat is not relevant because the typical CAGE tags are 27 nt long. Lukasz has some strange protocol though, so it is relevant to him with the long read lengths that he has.