Multiplexed Pair-End Sequences -- Barcode Sorting
3
1
Entering edit mode
10.5 years ago
Johnmu ▴ 20

Does there exist any tool to do barcode splitting of pair-end sequences?

I realise that FastX toolkit has a barcode splitter. However, it does not work with pair-end sequences since we would need to delete or keep both sequences in the pair.

Anyone know an free software that does this? If not I have have to code one up :(

rna paired barcode • 6.2k views
ADD COMMENT
1
Entering edit mode

Isn't fastx_splitter a perl-program? I think we should just add some code to it to allow for paired-end

ADD REPLY
0
Entering edit mode

Hi John, What's the possible cost for Multiplexing sequencing for 4096 samples? I am interested to one genomic region (350bp) in 4096 samples? I want to know the cost of this sequencing. Thanks.

ADD REPLY
0
Entering edit mode

You are posting to a very old thread, it is unlikely the original poster will read this.

ADD REPLY
0
Entering edit mode

In addition, I think it is best to simply ask a sequencing provider of your choice for a quote.

ADD REPLY
4
Entering edit mode
10.5 years ago
Yannick Wurm ★ 2.3k

For a similar issue, Keith suggested the following approach:

  1. join paired reads into single megareads (using Galaxy toolkit)
  2. do your thing (filtering or barcode splitting)
  3. split the concatenated megareads back into paired reads

cheers,
y.

ADD COMMENT
3
Entering edit mode
10.5 years ago
brentp 23k

I had the same problem with filtering paired-end reads. In the end, I just wrote a script to call the fastx-toolkit filter on both files and then further filter out reads that were removed from only one of the pairs. Since you know the files come out in the same order, you can do the filtering yourself without reading everything into memory.

So, yes, a custom script is likely your best bet as most existing tools only do a single-end at a time.

ADD COMMENT
1
Entering edit mode

Thanks for the answer, I'll see what I can do.

ADD REPLY
0
Entering edit mode
10.5 years ago

NovoBarCode handles paired end Illumina reads and works with a number of different barcoding schemes:

http://www.novocraft.com/userfiles/file/NovoBarcode.pdf

It's not open source, but is free for academic and non-profit use.

ADD COMMENT

Login before adding your answer.

Traffic: 2486 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6