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Search: Posts Made By: leftisthominid
Forum: General 03-30-2015, 11:54 AM
Replies: 0
Views: 1,859
Posted By leftisthominid
Calculating concentration of whole sample based on concentration of dilution

Hello, I submitted a plate of DNA samples diluted to ~50 ng/ul (based on nanodrop values) for picogreen assay to a core lab this morning. I am trying to figure out how to figure out my actual...
Forum: General 02-20-2015, 12:09 PM
Replies: 0
Views: 1,308
Posted By leftisthominid
OD 260/230 values for Affymetrix Axiom

I am getting ready to run some samples on an Affymetrix Axiom array.

The AxiomŽ 2.0 Assay Manual Workflow...
Forum: General 01-29-2015, 03:15 PM
Replies: 7
Views: 4,635
Posted By leftisthominid
Ineffective Zymo Clean and Concentrate-5 kit

Hello, I have used a Zymo Clean and Concentrate-5 sample kit on three of my DNA samples extracted from FTA cards. Each three samples started with 12 ul of DNA suspended in reduced EDTA 1× TE (10mM...
Forum: Bioinformatics 05-01-2014, 12:23 PM
Replies: 0
Views: 801
Posted By leftisthominid
Extracting SNP data from published genome sequences

I had a question about a project I am conceptualizing. Since I have no experience yet dealing with nuclear DNA, I have some questions.

I have SNP data on 64 samples from my population of interest...
Forum: Bioinformatics 06-19-2013, 01:08 PM
Replies: 0
Views: 1,168
Posted By leftisthominid
Has anyone else here used Mapping Iterative Assembler?

Hello, I have been using MIA package on some mtDNA library sequence, and I have noticed after I use the 'ma' tool to convert the maln assemblies from the 'mia' tool into ACE assemblies, in my output...
Forum: Bioinformatics 06-19-2013, 10:11 AM
Replies: 1
Views: 900
Posted By leftisthominid
Calculating and separating reads per chromosome

Hello, my lab just did some Illumina sequencing using mitochondrial bait.

I wanted map my to fastq files to the whole human genome, so I can fully determine the efficacy of the bait and determine...
Forum: Genomic Resequencing 06-19-2013, 09:57 AM
Replies: 4
Views: 11,306
Posted By leftisthominid
Calculating and separating reads per chromosome

Hello, my lab just did some Illumina sequencing using mitochondrial bait.

I wanted map my to fastq files to the whole human genome, so I can fully determine the efficacy of the bait and determine...
Forum: Illumina/Solexa 06-14-2013, 09:08 AM
Replies: 10
Views: 4,502
Posted By leftisthominid
I used bowtie2 to filter out off-bait target and...

I used bowtie2 to filter out off-bait target and then loaded results got a little better, but not much.

Gringer, is that vcftools modification customized or is it something that was already made?
Forum: Illumina/Solexa 06-13-2013, 09:41 AM
Replies: 10
Views: 4,502
Posted By leftisthominid
So, I ran unjoined sequences - problem remains ...

So, I ran unjoined sequences - problem remains
I used cutadapt to trim out short reads and <30 quality - problem remains
I used slightly stricter filter options in MIA (on non-cutadapt'd sequence)...
Forum: Illumina/Solexa 06-11-2013, 09:11 AM
Replies: 10
Views: 4,502
Posted By leftisthominid
fastq-join outputs three files: a fastq with...

fastq-join outputs three files: a fastq with joined reads, a fastq from file 1 of the unjoinables, and a fastq from file 2 with the unjoinables. All three are effectively single end reads after the...
Forum: Illumina/Solexa 06-10-2013, 02:16 PM
Replies: 10
Views: 4,502
Posted By leftisthominid
Forgot to post above. The fastq's that went into...

Forgot to post above. The fastq's that went into Mapping Iterative Assembler generally had FASTQC results like this
[PASS] Basic Statistics
[PASS] Per base sequence quality
[PASS] Per...
Forum: Illumina/Solexa 06-10-2013, 01:53 PM
Replies: 10
Views: 4,502
Posted By leftisthominid
mtDNA genome assembly problems

Hello, we recently paired sequenced a 94 mtDNA libraries on a Illumina HiSeq and I am now working on assembling the sequences, determining coverage, etc.

For the most part I have not done a lot of...
Forum: Bioinformatics 04-04-2013, 03:57 PM
Replies: 0
Views: 1,709
Posted By leftisthominid
Trying to get Altai Neanderthal chromosome 2 VCF, facing difficulties

Hello, I am trying to generate a vcf file from http://cdna.eva.mpg.de/neandertal/altai/bam/AltaiNea.hg19_1000g.2.dq.bam

I have downloaded it to the University of Florida's Fisher Bioinformatics...
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