Barcodes length in the split library

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Beatriz Gil Pulido

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Aug 15, 2016, 5:34:02 AM8/15/16
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Hi, 

I'm preparing some samples for an amplicon library using 454 service. I'm using a set of primers where the barcodes length are different. So, there are two types of barcodes: length 6bp or 8bp. I don't know if that might cause any problem in the split library step. I don't know if I can run the split_libraries.py command using two different MIDs length. 

Thanks, 


Colin Brislawn

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Aug 15, 2016, 1:03:58 PM8/15/16
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Hello Bea,

You should be able to run split libraries twice; once for samples with 6 bp barcodes, and again for samples with 8 bp barcodes. 

I hope this helps,
Colin

Beatriz Gil Pulido

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Aug 16, 2016, 5:15:42 AM8/16/16
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Hi Colin,

So, once I'll generate the two different outputs for the split library (depends on the bp barcode) how can I do for working with both data set together? The multiplex samples, with different barcodes length, are part of the same study so what I want to do is analyzed them all together. I've read something about merging OTU tables, for example. But I don't really if for this particular case, it'd be the same. 

Thanks. 

Bea. 

Colin Brislawn

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Aug 16, 2016, 12:56:33 PM8/16/16
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Hello Bea,

When running split libraries twice, make sure that each barcode is matched to its unique sample name. After running split libraries twice, you will have two seqs.fna file in which each Read has a unique sample name appended to the Read ID. Then you can safely concatenate the two files together using the linux 'cat' command. 
cat output1/seqs.fna output2/seqs.fna > combined_seqs.fna 

Then you can use combined_seqs.fna for downstream analysis and all your samples will be analized together.

Colin

Beatriz Gil Pulido

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Aug 16, 2016, 4:18:46 PM8/16/16
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Hi Collin, 

Thanks so much for tip. 


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