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Forum: Bioinformatics 04-21-2016, 12:40 AM
Replies: 0
Views: 667
Posted By dhatziioanou
counting Ns and gaps in scaffolds

Hello,

I have been trying to assemble some genomes and need a way to keep track of the number of gaps and NNs in my scaffolds. I've found ways to count everything else but not those.

I've been...
Forum: Bioinformatics 10-02-2015, 01:49 AM
Replies: 35
Views: 18,828
Posted By dhatziioanou
Hello, I know this is a pretty old thread but I...

Hello, I know this is a pretty old thread but I got the same problem now in 2015 and since I don't have any good quality data to use instead I had a little dig. The index error is a python error...
Forum: Bioinformatics 08-04-2015, 03:42 AM
Replies: 0
Views: 500
Posted By dhatziioanou
plain text blast conversion to Jamblast input

Hello,

Does anyone know how to convert blastp output in plain text format (m=0, default) to something Jamblast v1.10 will accept? Reblasting with the patched blastall, blastcl3 and blastpgp...
Forum: Sample Prep / Library Generation 05-27-2015, 11:30 PM
Replies: 2
Views: 892
Posted By dhatziioanou
Snap freeze in liquid nitrogen when you collect...

Snap freeze in liquid nitrogen when you collect it then put it straight into trizol and grind it with Qiagens fancy bead machine or manually grind it with a mortar and pestle on dry ice while keeping...
Forum: Sample Prep / Library Generation 05-22-2015, 05:41 AM
Replies: 2
Views: 1,862
Posted By dhatziioanou
Oh and its best to empty the tank out at night...

Oh and its best to empty the tank out at night just in case you do get any salt or something or other managing to grow in it or stick to the tank walls, its supposed to be a super sensitive and...
Forum: Introductions 05-22-2015, 05:12 AM
Replies: 3
Views: 1,576
Posted By dhatziioanou
So far the only sequenced genomes of closely...

So far the only sequenced genomes of closely related species I can find are 27-32 Mb but other slightly further related species range from 13-100 Mb.
It should be a diploid and I'm expecting plenty...
Forum: Sample Prep / Library Generation 05-21-2015, 05:50 AM
Replies: 2
Views: 1,862
Posted By dhatziioanou
As far as I recall (its been 2-3 years) we used...

As far as I recall (its been 2-3 years) we used to use milliQ water and changed it everyday before using it.
Forum: Introductions 05-21-2015, 04:56 AM
Replies: 3
Views: 1,576
Posted By dhatziioanou
Newbe struggling

Hello everyone,

I'm new to genome assemblies and am trying to patch together de novo a genome without an available reference (expected size 20-100 Mb).
I've got about 32 files of paired end...
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