Forum: Bioinformatics
08-04-2017, 11:38 AM
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Replies: 0
Views: 848
Where to download Drosophila Muller elements
Hi Everyone,
I would like to map DNA genomic sequences of a non-model insect species on muller elements from drosophila. My goal is to perform a comparative evolutionary analysis by identifying...
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Forum: De novo discovery
11-21-2016, 08:29 AM
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Replies: 0
Views: 5,375
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Forum: Bioinformatics
08-07-2016, 04:02 PM
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Replies: 0
Views: 2,229
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Forum: Bioinformatics
07-15-2015, 05:12 AM
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Replies: 2
Views: 2,372
Hi Linnea,
Thanks for the suggestion and the...
Hi Linnea,
Thanks for the suggestion and the article links. This should be extremely helpful, I am grateful! I had thought of the 'crap reads' in ChrY but I wasn't sure yet of how to handle them....
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Forum: Bioinformatics
07-14-2015, 11:35 AM
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Replies: 2
Views: 2,372
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Forum: Bioinformatics
08-21-2014, 01:23 PM
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Replies: 1
Views: 1,526
genome comparisons-identifying unique sequences
Hi everyone,
I have assembled de novo the genome of a non model organism, whose female has two strains. My goal is to identify unique sequences between the two types of females. That is to extract...
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Forum: Bioinformatics
03-18-2014, 12:22 PM
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Replies: 3
Views: 6,665
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Forum: Bioinformatics
03-18-2014, 12:06 PM
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Replies: 2
Views: 1,591
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Forum: Bioinformatics
03-11-2014, 11:07 AM
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Replies: 2
Views: 1,591
Problem running bedtools (fastFromBed)
Hi Everyone!
I have a gff file of the drosophila r5.48 genome, and the corresponding all chromosome fasta files.
I want to extract the DNA sequences into a fasta file based on the coordinates from...
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Forum: Bioinformatics
02-17-2014, 08:20 AM
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Replies: 4
Views: 2,167
The kind of summary stats I am aiming for or...
The kind of summary stats I am aiming for or rather looking to extract is kinda similar of what is outputted by blast2go, ie in terms of top hit species and species distribution.
So, I was wondering...
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Forum: Bioinformatics
02-15-2014, 09:42 PM
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Replies: 4
Views: 2,167
Blastn Results - analysis
Hi Everyone,
I have done some blasting on a draft genome that I assembled de novo(~300,000 contigs) and now I want to analyze the results. I used blastn, and I really want to see what was found in...
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Forum: Bioinformatics
01-21-2014, 12:29 PM
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Replies: 2
Views: 1,545
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Forum: Bioinformatics
01-21-2014, 10:30 AM
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Replies: 2
Views: 1,545
Site with raw reads of Drosophila Melanogaster
Hi Everyone,
I have assembled a draft genome de novo of a non model organism (insect). I would like to compare it with Drosophila melanogaster (similarities etc) My plan is to map the Drosophila...
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Forum: Bioinformatics
11-22-2013, 07:50 AM
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Replies: 8
Views: 4,365
Gene Ontology analysis tools
Hi Everyone,
I desperately need your expertise advise on this :)
I have a assembled a genome de novo, and I would like to run gene ontology analysis on it. I have around 300k contigs. What...
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Forum: Bioinformatics
08-12-2013, 01:59 PM
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Replies: 2
Views: 2,736
Soap De Novo assembly interpretation
Hello!
I have run soap de novo on my assembly, and I have used different kmers. I have 12 assemblies and I need to choose the best one out of those 12.
There are around 21 files created in each...
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Forum: Bioinformatics
08-12-2013, 01:46 PM
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Replies: 2
Views: 1,625
Galaxy in Linux
Hello Everyone,
Quick question. I have used galaxy before to run blastn and blastx (the gui web version). I know want to try using Galaxy installed in linux (the command mode version).
Does...
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Forum: Bioinformatics
08-02-2013, 03:38 PM
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Replies: 1
Views: 2,919
Velvet assembly stats
Hi everyone,
My question is about the analysis of velvet denovo assembly.
Are the statistics printed out on the Log file the final real statistics of the assembly?
How does one go about to...
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Forum: Bioinformatics
07-06-2013, 11:41 AM
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Replies: 2
Views: 1,953
help...
Hi again, I am guessing there might not be a specific bioinformatics tool that can accomplish the goal of comparing two genomes. So, re-phrasing my question, what could be a possible pipeline that...
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Forum: Bioinformatics
07-03-2013, 10:51 PM
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Replies: 2
Views: 1,953
Genome comparison
Hi wise people.
I have assembled two genomes of a non-model organism via de novo assembly, a male and female assembly. I want to compare the male and female genome to check out what differences...
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Forum: Bioinformatics
07-03-2013, 10:44 PM
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Replies: 6
Views: 4,214
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Forum: Bioinformatics
06-28-2013, 12:33 PM
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Replies: 6
Views: 4,214
help using velvet for de novo assembly
Hi everyone, i'm trying to run de novo assembly using velvet on short (100bp long) paired end reads.
I first ran velveth and it created only two files named: Log and Sequences.
It also gave me...
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Forum: Bioinformatics
06-05-2013, 09:33 AM
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Replies: 7
Views: 11,245
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Forum: Bioinformatics
06-04-2013, 02:35 PM
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Replies: 5
Views: 1,803
I am first starting with a small group ie 10...
I am first starting with a small group ie 10 sequences, each sequence is approx 150bp (ie the left flank region + repeat motif + right flanking region). The size of one of the popns that I want to...
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Forum: Bioinformatics
06-04-2013, 12:42 PM
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Replies: 5
Views: 1,803
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Forum: Bioinformatics
06-04-2013, 12:06 PM
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Replies: 5
Views: 1,803
microsatellite query
Hello wise people!
I have approx 10,000 microsatellites that I obtained from some assembled dna of a non-model organism. I selected a subset of the microsatellites including 50bp of the right and...
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