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Forum: Bioinformatics 08-04-2017, 10:38 AM
Replies: 0
Views: 640
Posted By NGS_New_User
Question 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...
Forum: De novo discovery 11-21-2016, 07:29 AM
Replies: 0
Views: 3,000
Posted By NGS_New_User
Exclamation Question regarding Zygosity variant calling interpretation - homozygote variants

Hi everyone,

I have assembled the genome of a non-model organism - insect (de novo genome assembly) and performed read mapping to it. I am currently in the process of performing a variant...
Forum: Bioinformatics 08-07-2016, 03:02 PM
Replies: 0
Views: 1,563
Posted By NGS_New_User
Exclamation Question regarding uploading genome to GenBank using tbl2asn

Hi everyone,

I am preparing a de novo assembled genome to upload into Genbank. I have followed the instructions in the website as indicated in the tbl2asn documentation and have successfully been...
Forum: Bioinformatics 07-15-2015, 04:12 AM
Replies: 2
Views: 1,795
Posted By NGS_New_User
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....
Forum: Bioinformatics 07-14-2015, 10:35 AM
Replies: 2
Views: 1,795
Posted By NGS_New_User
Question Extracting sex chromosomes from sequenced genomic DNA reads or assembled genome

Hi everyone.

I have two sets of data; male and female (Illumina sequenced, PE reads, ~300 million each, 100bp) of a non-model organism (insect). Since it has no reference genome I performed a de...
Forum: Bioinformatics 08-21-2014, 12:23 PM
Replies: 1
Views: 1,229
Posted By NGS_New_User
Exclamation 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...
Forum: Bioinformatics 03-18-2014, 11:22 AM
Replies: 3
Views: 5,941
Posted By NGS_New_User
Question Removing contaminants (bacteria, phage) in genomic dna sequences

Hi Everyone,
I have dna, paired-end genomic sequences that I want to perform de novo assembly on, but I want to 'clean' them up first ie remove contaminants, before de novo assembly.
I have already...
Forum: Bioinformatics 03-18-2014, 11:06 AM
Replies: 2
Views: 1,296
Posted By NGS_New_User
Thanks, I will try to look for it

Thanks, I will try to look for it
Forum: Bioinformatics 03-11-2014, 10:07 AM
Replies: 2
Views: 1,296
Posted By NGS_New_User
Exclamation 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...
Forum: Bioinformatics 02-17-2014, 07:20 AM
Replies: 4
Views: 1,592
Posted By NGS_New_User
Exclamation 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...
Forum: Bioinformatics 02-15-2014, 08:42 PM
Replies: 4
Views: 1,592
Posted By NGS_New_User
Exclamation 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...
Forum: Bioinformatics 01-21-2014, 11:29 AM
Replies: 2
Views: 1,214
Posted By NGS_New_User
Thank you so so much GenoMax, I really do...

Thank you so so much GenoMax, I really do appreciate it :-)
Forum: Bioinformatics 01-21-2014, 09:30 AM
Replies: 2
Views: 1,214
Posted By NGS_New_User
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...
Forum: Bioinformatics 11-22-2013, 06:50 AM
Replies: 8
Views: 3,855
Posted By NGS_New_User
Question 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...
Forum: Bioinformatics 08-12-2013, 12:59 PM
Replies: 2
Views: 2,286
Posted By NGS_New_User
Exclamation 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...
Forum: Bioinformatics 08-12-2013, 12:46 PM
Replies: 2
Views: 1,405
Posted By NGS_New_User
Question 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...
Forum: Bioinformatics 08-02-2013, 02:38 PM
Replies: 1
Views: 2,409
Posted By NGS_New_User
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...
Forum: Bioinformatics 07-06-2013, 10:41 AM
Replies: 2
Views: 1,674
Posted By NGS_New_User
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...
Forum: Bioinformatics 07-03-2013, 09:51 PM
Replies: 2
Views: 1,674
Posted By NGS_New_User
Exclamation 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...
Forum: Bioinformatics 07-03-2013, 09:44 PM
Replies: 6
Views: 3,415
Posted By NGS_New_User
Thanks for the suggestions! I do appreciate them!...

Thanks for the suggestions! I do appreciate them! I am going to try them, hopefully no errors will pop up :)
Forum: Bioinformatics 06-28-2013, 11:33 AM
Replies: 6
Views: 3,415
Posted By NGS_New_User
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...
Forum: Bioinformatics 06-05-2013, 08:33 AM
Replies: 7
Views: 10,258
Posted By NGS_New_User
Yes, it has a phenotypic male and female in its...

Yes, it has a phenotypic male and female in its reproductive cycle
Forum: Bioinformatics 06-04-2013, 01:35 PM
Replies: 5
Views: 1,472
Posted By NGS_New_User
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...
Forum: Bioinformatics 06-04-2013, 11:42 AM
Replies: 5
Views: 1,472
Posted By NGS_New_User
I found a program online called phobos, that's...

I found a program online called phobos, that's the one I used. There is also TRF and msat commander but I haven't tried using those ones yet.
Forum: Bioinformatics 06-04-2013, 11:06 AM
Replies: 5
Views: 1,472
Posted By NGS_New_User
Exclamation 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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