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Old 08-22-2016, 12:10 PM   #1
MLog
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Location: Russia

Join Date: Jan 2010
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Default script for checking barcode compatibility

Hi everyone,

a colleague of mine wrote a script that checks the compatibility of barcodes used in different sample prep kits for Illumina (Truseq LT/HT, Nextera, Nugen) - for the case when we need to pool samples made with different kits on one Hiseq lane or Miseq/Nextseq run. (We consider as compatible those barcodes that have edit distance greater or equal to 3.)
I find it very helpful so I took the liberty to post the link - http://makarich.fbb.msu.ru/shelkmike...check_eng.html
I hope, it will be useful for many other Illumina users.

(I know that Illumina does not support pooling different libraries, e.g. Nextera and Truseq or Truseq LT and Truseq HT, but we do this and this works fine).
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Old 08-22-2016, 10:45 PM   #2
JakobHedegaard
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Default

Hi, thank you very much for sharing this.
I have made a simple and a bit rough R-script (attached) to compare two list of indexes and return a similarity matrix, which can be used to select index combination with at least 3 bases difference.
Presently I am trying to implement a "base-balance check" to verify the G/T vs A/C balance. Are you considering to implement this in your tool?
Another nice add-on to your tool would be the possibility to upload lists of indexes.
Cheers,
/Jakob
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File Type: txt compare_index_R.txt (7.6 KB, 27 views)
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