What kind of mapping either gapped or ungapped mapping is better for RNA seq

Question

[Fizzah]

Hello there, I am using RNA seq fro cotton data and generated paired end reads of 150bp in length. I need help regarding which type of mapping will be best for dealing RNA seq data.. Should I opt for Gapped or ungapped one.. To my knowledge gapped mapping is recommended while dealing with genomic data and for transcriptomic data mapping ungapped is used.

I might be wrong so need help..

Also suggest some mapping software's for reads 150bp in length. I tried to use tophat but its not quite good.

Regards
Fizzah

Answer 1

[ATpoint]

You cannot choose. The tool you use imposes that on you, and most do gapped alignments to allow for small variants in the data. After all the reference genome/transcriptome is just a reference, yet individuals have genetic variation. Use any of the mentioned tools, with default settings and/or following their manuals and you will be fine.

Edit: In my understanding ungapped alignments do not really exist anymore in NGS analysis these days (correct me if I am wrong). bowtie (aka "bowtie1") did it and it was designed for very short reads (like 25bp or 36bp) in the early days of NGS. These reads have the problem that the very short size makes them hard to map as short reads are not unique and prone to be multimappers. If you additionally allow gaps the potentials origins even pile up more so it probably hurts more than it benefits. So (and I am just guessing) ungapped alignment was performed back in the days. Later tools like bowtie2 then allowed gapped alignments as technology (and by this read length) improved and the problems associated with the very short reads became less critical.

[Fizzah]

ok got your point. Thank your for your help

Answer 2

[rpolicastro]

You should use a splice-aware aligner such as STAR. If all you need is to quantify gene and/or transcript counts you can use Salmon instead (recommened).

[Fizzah]

Can you also explain about gapped and ungapped mapping? which one should I go with?