Sangar split - Revision history

Raj at 17:58, 7 April 2010

2010-04-07T17:58:55Z

← Older revision		Revision as of 17:58, 7 April 2010
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			[[Category:Bioinformatics]]
	<pre>		<pre>
	Dear Rajkumar,		Dear Rajkumar,

Raj at 17:57, 7 April 2010

2010-04-07T17:57:25Z

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	* Script		* Script
	** [[read_split]]		** [[read_split.pl]]

Raj at 17:57, 7 April 2010

2010-04-07T17:57:17Z

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	* Script		* Script
	** [[~~sanger_split~~]]		** [[read_split]]

Raj at 16:27, 7 April 2010

2010-04-07T16:27:28Z

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	Sincerely,		Sincerely,
	Raja		Raja
			Raja Ragupathy PhD, AAFC-Cereal Research Centre, University of Manitoba Campus, Winnipeg, Manitoba Canada R3T2M9 Phone: 204-899-2612 (M)
	</pre>		</pre>
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			* Script
			** [[sanger_split]]

Raj: Created page with '

 Dear Rajkumar,  Good day.   For my current project, I need some bioinformatics support. Please treat the data confidential since we have to publish it. I have 9 sets of fil…'

2010-04-07T16:17:42Z

Created page with '<pre> Dear Rajkumar, Good day. For my current project, I need some bioinformatics support. Please treat the data confidential since we have to publish it. I have 9 sets of fil…'

New page

<pre>
Dear Rajkumar,

Good day.

For my current project, I need some bioinformatics support. Please treat the data confidential since we have to publish it.
I have 9 sets of files each with ~10K fasta sequences (Sanger). However, some query sequences are ‘0’ in length (nearly 4% of total 80K reads). For example, please see the following set of 5 sequences where (0) represents absence of sequence data.

>FLXa1302.ePiR_A01 (0)
>FLXa1302.EPiF_A02 (0)
>FLXa1302.ePiR_A02 (0)
>FLXa1302.EPiF_A03 (0)
>FLXa1302.ePiR_A03 (0)

I am attaching a file with the mixture of these (0 bp) reads with normal fasta sequences.
I wish to group reads with sequences and reads without sequences into two individual set of files for further analysis. Also, I wish to have subset of sequences which are more than 80 bp in length. I don’t want to delete them. I want 3 subsets from each set of sequences. i.e

Reads (0bp)
Reads from 1 bp to 80 bp in length
Reads with more than 80 bp

I am attaching the first file. Could you please try to segregate that into three files as mentioned above? Once I get the result for this file I will go through it, then I will send the remaining files.
Thanks for your time,

Sincerely,
Raja
</pre>