How To Demultiplex Mate Paired Reads When You Have Only One Index?

Question

[Sameet]

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.

[Manu Prestat]

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

[Michael]

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 ;)).

[Doctoroots]

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

[Sameet]

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

Answer 1

[Doctoroots]

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.

Answer 2

[Swbarnes2]

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.

[Sameet]

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.