comparing mapping results in two tools

Question

[zizigolu]

Friends,

I aligned my reads in both bowtie2 and tophat. Now how I can see and compare the mapping result in two mentioned tools?

Thank you

[AndreiR]

hello,

what version of bowtie you used in tophat? and what version of tophat you have used?

[zizigolu]

bowtie2 and tophat2

Answer 1

[Antonio R. Franco]

Why do you want to do that ?. It is non sense..

TopHat will do a initial mapping using bowtie2 (so you get the same that using bowtie2 alone), and it will do a segmentation of the unmapped sequences to try a new mapping using bowtie2 again to detect spliced sequences

[zizigolu]

thank you Antonio,

sorry, how i can be aware of rate of the reads which aligned in multiple place on genome in tophat output?

[Devon Ryan]

Tophat2 will give them a MAPQ or 0, 1, 2, or 3. Non-multimappers are given a MAPQ of 50 (last time I looked at least).

[zizigolu]

thank youuuuuu Devon

[Antonio R. Franco]

Take a look to this page

Inside the SAM file, you can read a FLAG value which is interpreted by the page shown above. It will be useful for you

Answer 2

[Prakki Rama]

If you have a sam/bam file, you can compare which mapping tool could align more number of reads. properly and improperly paired reads and overall number of reads aligned would help you.