visualisation tool for paired-end, to find the mate?

[Fad2012]

Hello all

I am looking for a visualisation tool to explore a large set of paired-end sequence data and be able to find the mate of a certain read. I have tried IGV (Integrative genomics viewer), but the problem with IGV that I couldn't find the mate of the read, it could display the reverse and forward reads in two different coolers, but it doesn't recognise the the forward mate of a reverse read or vice versa. Any suggestion to visualise the paired-end reads with a possibility to recognise the mate of any read ?

Many thanks

[GenoMax]

Hello all

I am looking for a visualisation tool to explore a large set of paired-end sequence data and be able to find the mate of a certain read. I have tried IGV (Integrative genomics viewer), but the problem with IGV that I couldn't find the mate of the read, it could display the reverse and forward reads in two different coolers, but it doesn't recognise the the forward mate of a reverse read or vice versa. Any suggestion to visualise the paired-end reads with a possibility to recognise the mate of any read ?

Many thanks

Did you right-click on the read you want to find the mate of and then select the "go to mate" or "view mate region in split screen"?

http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/NGS_splitmenu.jpg

Alternatively you can try the "paired view" as shown on the help page. http://www.broadinstitute.org/igv/alignmentdata

[Fad2012]

Dear GenoMax

Thanks very much for your reply, yes indeed, i tried both options you mentioned but they don't work properly with a large set of data, as you have to manually go to each pair and choose the "go to mate", even this does not work precisely; the software would highlight the selected read but not the paired one most of the time.Moreover the highlighting colour system is not very practical as it keeps vary and two pairs might take the same colour, so imagine how confusing would it be if you are dealing with million of reads. I also tried to split the reads into two screens, but this did not add and value to the whole process, and still very difficult to find the paired-end, i tried to sort colour alignment by reads, insert size, no color ... etc, nothing worked. The last thing i tried was the view as pairs, this did work with around 2% of the whole data, because if you have a high depth of coverage the reads will be very close to each other and the line by which the software like the read will easily get lost.

I am looking for a more practical tool to do this job, so i can examine a set of reads out of million of reads precisely, and accurately!

Many thanks

[GenoMax]

Are you observing that the paired ends that you have are not mapping within the expected distance (~200-400 bp) leading to a problem with the visualization or are these paired-ends from a longer mate pair library?

Can you add some clarification on the "practical tool" part? What exactly are you trying to look at? Perhaps you could filter your bam to remove reads you are not interested in.

[Fad2012]

I want to analyse the sequences of the reads aligned at a specific location of the genome. At this specific location i have a large depth of coverage, and then i want to study how the reads are corresponding to their mates, that is i want to see if there is any correlation between the insertion distance and the location (Sequences) . So i am trying to collect all the reads aligned at this specific position, at which IGV demonstrates a large amount of aligned reads!! I am not sure how to attach a photo here, so it would be clearer ?

many thanks

[GenoMax]

I am not sure how to attach a photo here, so it would be clearer ?

many thanks

Use "snipping tool" (Windows), "grab" (OS X) or an appropriate tool for your OS to capture a screen shot from IGV window. Save file in "png" format.

When editing your post on SeqAnswers, click the "Go Advanced" button. You can then click on the "paper clip" icon at the top of the editing tools row which will open a new window. This window allows you to attach various files (including images) to your post.

[Fad2012]

Thanks GenoMax

Find the attached photo please! i am trying to answer a question of whether the reads under the red circle correspond to the blue circle or the green one, and then want to obtain the sequences of these reads, but as i told you it is very tricky in IGV!

[maubp]

You might prefer the interface in Tablet, perhaps very zoomed out?

http://bioinf.hutton.ac.uk/tablet/download.shtml