Question: How can I group files by barcode?
0
gravatar for jixueli
3 months ago by
jixueli10
jixueli10 wrote:

I have thousands sequencing files, in those files, there are 4 different files: three different barcodes and one background, I try to split them by "barcode spliter" application, but it's not work because the barcodes randomly exist in the sequence text, I think perhaps I need a alignment application to recognize my barcode in the text files, can any suggestion given to solve this problem?

alignment • 127 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by jixueli10
1
gravatar for jixueli
3 months ago by
jixueli10
jixueli10 wrote:

Hi, Thanks for your help. I have solved this problem by use tools of Galaxy-filter and sort-select by (barcode sequence){1,}, then trim them by using python newsequencing=myfile.readline(position1:position2). Thanks!

ADD COMMENTlink written 3 months ago by jixueli10

Glad you found a solution that works!

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

True, the barcode splitting will not work for your use case. Instead, try the tool NGS: Mothur > Trim.seqs.

There is a link near the bottom of the tool form to the Mothur wiki that can help with usage. And a Galaxy tutorial using the tool suite as an example is here: http://galaxyproject.github.io/training-material/topics/metagenomics/

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson23k
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