Question: How To Demultiplex Mate Paired Reads When You Have Only One Index?
2
gravatar for Sameet
7.1 years ago by
Sameet290
Sameet290 wrote:

Hi,

I had a multiplexed RNA-Seq run on Hi-Seq machine. The index was part of the Read1, but the Read2 has no index. How can I separate the reads in the Read2 file.

EDIT: I have a Read 1 file R1.fq where the first 6 bases are the barcode. I have R2.fq (the mate file) which has no barcode. I know I can use the fastx barcode splitter to separate the reads from the R1.fq, which I have done. I am not sure how I can now use this R1_sample.fq to fish the specific mate reads from the R2.fq.

I hope this question is now clearer.

paired rna • 4.0k views
ADD COMMENTlink modified 7.1 years ago by Swbarnes21.4k • written 7.1 years ago by Sameet290
2

You may need to provide more details if you want relevant answers...

ADD REPLYlink written 7.1 years ago by Manu Prestat3.9k

I believe if you give an example of your files, like 10 lines each, with some related reads, you'd have at least 2 viable solutions within few hours as I know this community (just trying to motivate ;)).

ADD REPLYlink written 7.1 years ago by Michael Dondrup45k

i would change the title to be a bit more specific, something like : how to demultiplex paired end reads with one index file?

ADD REPLYlink written 7.1 years ago by Doctoroots760

@doctoroots is correct. That is the question i want to ask? Sorry for being vague earlier. I will edit the question to reflect this.

ADD REPLYlink written 7.1 years ago by Sameet290
3
gravatar for Doctoroots
7.1 years ago by
Doctoroots760
Doctoroots760 wrote:

Considering the details given, i dont have alot to offer, but you can try this tool :

FastqMultx

with the -g option for the reads index file. it should demultiplex both files.

ADD COMMENTlink written 7.1 years ago by Doctoroots760
1
gravatar for Swbarnes2
7.1 years ago by
Swbarnes21.4k
Swbarnes21.4k wrote:

Reads should have the same coordiantes in their name as their mate. If you know which coordinates belong to which index, you can use those names to pull out the reads from the read 2 file.

ADD COMMENTlink written 7.1 years ago by Swbarnes21.4k

Yes i was thinking along same line, but the answer given by @doctoroots pretty much solved my problem. It does seem to be a pretty decent tool. The help is a bit wanting, but it will do the job for you.

ADD REPLYlink written 7.1 years ago by Sameet290
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