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Forum: Academic/Non-Profit Jobs 04-18-2012, 07:45 AM
Replies: 0
Views: 2,355
Posted By seqseq
Bioinformatics postdoc: Plant genomics (Barcelona, Spain)

The Department Prof. Lehrach, Group Dr. H. Himmelbauer invites applications for the following open position (funding until September 30th 2014):

Postdoc Bioinformatics / Computational Biology
(E...
Forum: Bioinformatics 03-25-2010, 02:00 AM
Replies: 11
Views: 4,012
Posted By seqseq
You are referring to this manual file, right? ...

You are referring to this manual file, right?
http://xyala.cap.ed.ac.uk/Gene_Pool/454_software/Version_2.3/SW-Manual_PartC_Assembler-Mapper-SFFTools_Oct2009.pdf

There is a decription of the...
Forum: Bioinformatics 10-21-2009, 10:27 AM
Replies: 22
Views: 16,412
Posted By seqseq
Great! The first part could be shortened into:...

Great! The first part could be shortened into: awk '{sum += $0; print $0, sum}'

So in total:
sort -rn contig_lengths.txt | awk '{sum += $0; print $0, sum}' | tac | awk 'NR==1 {halftot=$2/2}...
Forum: Bioinformatics 10-16-2009, 06:06 AM
Replies: 22
Views: 16,412
Posted By seqseq
What about the awk experts out there? Any idea...

What about the awk experts out there? Any idea for the direct command-line version without script? (you have to store the script somewhere, and if you are using another computer you don't have it at...
Forum: Bioinformatics 10-16-2009, 05:18 AM
Replies: 22
Views: 16,412
Posted By seqseq
It comes up in several occasions, e.g. a file...

It comes up in several occasions, e.g. a file containing

contig1 length=1000 reads=582
contig2 length=1500 reads=900
contig3 length=1400 reads=766
...

I want to do something like:
$ cut...
Forum: Bioinformatics 10-16-2009, 05:02 AM
Replies: 22
Views: 16,412
Posted By seqseq
Well, I am looking for a Unix command-line...

Well, I am looking for a Unix command-line solution.. (btw if I understand your code correctly it is calculating the median, but median is not the same as N50 size)
Forum: Bioinformatics 10-16-2009, 03:40 AM
Replies: 22
Views: 16,412
Posted By seqseq
Unix one-line command for N50 size

Is there a good one-liner for calculating the N50 size of a list of contig sizes? Average size is easy with awk but I didn't manage to find an easy way for the N50 size so far. Thanks!
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