Question: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
2
gravatar for Tianyang Li
6.3 years ago by
Tianyang Li490
Beijing, China
Tianyang Li490 wrote:

Hi,

I'm wondering if it's OK to use one end of a set of paired-end reads as a set of single reads?

I just want to get a single read data set of a sample, but currently there's only paired-end data available. Mapping isn't that crucial to me right now.

I don't have a very in depth knowledge of the sequencing process, but it makes sense to me.

Thanks!

read paired-end • 1.4k views
ADD COMMENTlink modified 6.3 years ago by Mitchell40 • written 6.3 years ago by Tianyang Li490

Please be more context specific. Current answers assume you are performing mapping.

ADD REPLYlink written 6.3 years ago by Mitchell40

I've edited it, I'm more interested in generating a single read data set.

ADD REPLYlink written 6.3 years ago by Tianyang Li490
7
gravatar for Jorge Amigo
6.3 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

of course it is OK, if with OK you mean that you aim to obtain single end results. the idea of a paired-end experiment is basically to improve the quality of the mapping process, hence you'll be more confident on your BAM alignments specially on difficult regions to sequence. after all, the paired-end reads alignment is no other than mapping each set independently, and then perform a pairing between all those results removing from final BAM all previous reads that don't match the pairing requirements. it's like a quality control step which you may avoid if desired, although you'll be lowering the power of the experiment.

ADD COMMENTlink written 6.3 years ago by Jorge Amigo11k

+1. "The idea of a paired-end experiment is basically to improve the quality of the mapping process". Some folks just don't get this idea :) !.

ADD REPLYlink written 6.3 years ago by Khader Shameer17k
0
gravatar for Conan
6.3 years ago by
Conan20
Beijing
Conan20 wrote:

IMO maybe it's feasible to map single ends data for SNP calling. But for SV calling or the data is RNA-Seq you'd better mapping reads with pairs.

ADD COMMENTlink written 6.3 years ago by Conan20
1

that's a generally spread thought which I don't share. good SNP calling depends on good mapping quality as much as SV calling, but as we are so used in research to have so many false positives we tend to feel fine with all those filters we have to apply afterwards. the more effort you do to increase the mapping quality, the best results you'll obtain when calling variants. it's the trade-off you have to continuously balance through all your ultrasequencing experiments.

ADD REPLYlink written 6.3 years ago by Jorge Amigo11k
0
gravatar for Mitchell
6.3 years ago by
Mitchell40
Mitchell40 wrote:

Why would you want to do this? If you're assembling best to use paried-end.

ADD COMMENTlink written 6.3 years ago by Mitchell40

I'm trying to verify a method for RNA-Seq analysis, but the amount of data is limited.

ADD REPLYlink written 6.3 years ago by Tianyang Li490

Hey Mitchell. Welcome to biostar. Just a little reminder for future. These kind of question/comments are better added as a 'comment' to the original question or another answer. Not as an 'answer' itself.

ADD REPLYlink written 6.3 years ago by Obi Griffith17k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1726 users visited in the last hour