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Old 10-13-2011, 03:16 AM   #1
Giorgio C
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Default Demultilplexing Sequences according to barcode --- Homemade script

Hy,

i need to make a script (in perl) for demultilpexing sequences and splitting and sorting them according to the barcode/Mid [Just starting from a fasta file].
I know there are a lots of tool for this purpose but i need to do this for my Ph.D. Can anyone help me or give me some suggestions ?

it would be very appreciate if anyone give me some advices.

Thanks,
Giorgio
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Old 10-13-2011, 05:41 AM   #2
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What's the problem with using the tools that are already available?
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Old 10-13-2011, 06:12 AM   #3
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My suggestion is to tell the people in charge of your Ph.D. that they are wasting your time and their grant money and if they want to publish in high impact journals, be awarded competitive grants and educate the next generation of top scientists they should promote their young scientists to do original research using the best tools available. Seriously there are a lot of bad ideas on graduate education and you would be doing a favor to future students to push the level of teaching up a notch.

That's maybe a productive exercise for a intro course to Perl, but clearly not something someone should have to do for a Ph.D.
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Old 10-13-2011, 07:35 AM   #4
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Perhaps Giorgio is looking to create a parser for a special situation (where the tags may be embedded in the sequence read or some variation of that idea) and do not follow standard protocol.
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Old 10-14-2011, 01:31 AM   #5
Giorgio C
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Hi ,

thank you for your replies. I know there are a lot of tool, very good. But in my situation i need to do it for an "exame" of the Ph.D. and dear ETHANol unfortunately here nobodies will teach teach me nothing so i need to learn all by myself. I don't know why but here bioinfomtatiscians are very jealous of their knowledges. So if you have a suggestion, or something to study etc.etc. i'd appreciate very much. I have not a particular situation only need to create a little script to split sequences according to the first 10 nucleotide (MID).

I know may seem a waste of time, but i need to do it, and i can't say nothing


However thanks to all
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Old 10-14-2011, 06:10 AM   #6
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Quote:
Originally Posted by Giorgio C View Post
Hi ,

thank you for your replies. I know there are a lot of tool, very good. But in my situation i need to do it for an "exame" of the Ph.D. and dear ETHANol unfortunately here nobodies will teach teach me nothing so i need to learn all by myself. I don't know why but here bioinfomtatiscians are very jealous of their knowledges. So if you have a suggestion, or something to study etc.etc. i'd appreciate very much. I have not a particular situation only need to create a little script to split sequences according to the first 10 nucleotide (MID).

I know may seem a waste of time, but i need to do it, and i can't say nothing


However thanks to all
I'm not a perl user so my terminology may be wrong, but ideally you'll have some sort of unique character or group of characters prior to the first 10 nucleotides (ie, a "/0:" or something like that). If so, you could create a separate array for each barcode, find the first 10 nucleotides after the unique character, and then have it put that read in the respective array. Then you can output each array in a separate file. Again, I don't use perl, but the only things you'll need to learn how to do are to input the data, create arrays (make sure they are big enough if they don't easily grow in size with perl), learn how to find the unique character, write basic loops to go through each read and have the read entered in the correct array (create a separate array for "unknown"), and then learn how to output the array.

This is assuming you have a single read with a barcode and not paired-end reads.
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Old 10-14-2011, 06:16 AM   #7
GenoMax
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Can you say something about your past experience with computer programming?

It is not clear from your posts if you are a novice or if you are actually asking for advice on how best to do this using perl?
Quote:
Originally Posted by Giorgio C View Post
Hi ,

thank you for your replies. I know there are a lot of tool, very good. But in my situation i need to do it for an "exame" of the Ph.D. and dear ETHANol unfortunately here nobodies will teach teach me nothing so i need to learn all by myself. I don't know why but here bioinfomtatiscians are very jealous of their knowledges. So if you have a suggestion, or something to study etc.etc. i'd appreciate very much. I have not a particular situation only need to create a little script to split sequences according to the first 10 nucleotide (MID).

I know may seem a waste of time, but i need to do it, and i can't say nothing


However thanks to all

Last edited by GenoMax; 10-14-2011 at 06:20 AM.
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Old 10-14-2011, 06:29 AM   #8
Giorgio C
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@Heisman : Thank you for your suggests in building the algorithm, i will try this way first.

@GenMax: I'm now beggining to learn syntax in perl and i have only some experience with PHP but in this case i need to write the script specifically in perl; i know it's obviously difficult also to suggest me something, but first or after i needed to begin . So if you have any advices i'll follow its.
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Old 10-14-2011, 06:40 AM   #9
GenoMax
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If you can spare the time and want to learn this right then I suggest starting with these two books (both by James Tisdall, O'Reilly Pub):

Beginning perl for bioinformatics
Mastering perl for bioinformatics

If you are in a hurry then consult resources like:

http://learn.perl.org/tutorials/
http://www.perlmonks.org/?


Quote:
Originally Posted by Giorgio C View Post
@GenMax: I'm now beggining to learn syntax in perl and i have only some experience with PHP but in this case i need to write the script specifically in perl; i know it's obviously difficult also to suggest me something, but first or after i needed to begin . So if you have any advices i'll follow its.
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Old 10-14-2011, 07:17 AM   #10
Giorgio C
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Grazie 1000,

GenoMax
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