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Search: Posts Made By: brachysclereid
Forum: Ion Torrent 05-01-2013, 12:33 PM
Replies: 4
Views: 6,467
Posted By brachysclereid
MiSeq versus Ion

I am quite interested in the same questions as in sfyoung's original post.

Did you buy an instrument? Are you happy with the results?
Forum: Illumina/Solexa 12-28-2012, 04:14 PM
Replies: 9
Views: 2,629
Posted By brachysclereid
SNP calling between samples....in a polyploid

Thanks for all the suggestions. I will check out Cortex. Do you think it can handle polyploids?
Forum: Illumina/Solexa 12-19-2012, 03:25 PM
Replies: 9
Views: 2,629
Posted By brachysclereid
Is there a way to call SNPs between samples with...

Is there a way to call SNPs between samples with samtools mpileup or GATK?
Forum: Illumina/Solexa 12-19-2012, 03:12 PM
Replies: 9
Views: 2,629
Posted By brachysclereid
Surely there is something free from academic labs...

Surely there is something free from academic labs that will do this
Forum: Illumina/Solexa 12-19-2012, 03:02 PM
Replies: 9
Views: 2,629
Posted By brachysclereid
SNP calling between samples....in a polyploid

I should also add that I am trying to call SNPs either without a reference genome or with the diploid version of a polyploid I am working with.
Forum: Illumina/Solexa 12-19-2012, 12:46 PM
Replies: 9
Views: 2,629
Posted By brachysclereid
SNP calling

Reference-based SNP callers work by comparing the sequence aligned to the reference. Are there any tools/piplines that will call SNPs between aligned files? In my case I am interested in calling SNPs...
Forum: Sample Prep / Library Generation 11-14-2012, 01:06 PM
Replies: 1
Views: 3,579
Posted By brachysclereid
TruSeq Custom Amplicon - Extension-Ligation Step

Does anyone have a suggestion for an enzyme cocktail to perform the extension-ligation step similar to what is shown in the Illumina TruSeq Custom Amplicon workflow step 2...
Forum: Bioinformatics 01-09-2012, 02:26 PM
Replies: 3
Views: 3,196
Posted By brachysclereid
who coined RNAseq? RNAseq as an alignment first approach only

Yes. The fact that RNA-seq stands for RNA-SEQuencing was not lost to me. However, initially the high depth sequencing reads were aligned to a reference genome and thus RNA-seq became synonymous with...
Forum: Bioinformatics 01-09-2012, 12:03 PM
Replies: 3
Views: 3,196
Posted By brachysclereid
who coined RNAseq? RNAseq as an alignment first approach only

Hi,
I have some questions regarding semantics surrounding the term RNAseq:

1. Who coined RNAseq? I was under the impression it was:

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B....
Forum: Bioinformatics 01-07-2012, 09:52 AM
Replies: 2
Views: 4,367
Posted By brachysclereid
kmer content in the first bases of Illumina sequence

I have seen odd kmer content in the first bases of Illumina reads in my data and others. Does anyone have an idea about why this is? The barcodes were trimmed already by the Cassava pipeline. Here...
Forum: Bioinformatics 12-14-2011, 07:07 AM
Replies: 5
Views: 2,634
Posted By brachysclereid
building a cladogram with 100,000 sequences

Thanks for all the advice. It will take a while to sort through all the possibilities. Perhaps clustering first will be a good approach.

I'll make a post if I can get something to work. In the...
Forum: Bioinformatics 12-10-2011, 02:03 PM
Replies: 5
Views: 2,634
Posted By brachysclereid
building a cladogram with 100,000 sequences...

Are there any tools capable of performing multi sequence alignment and tree construction that can handle up to 100,000 sequences?
Forum: Bioinformatics 12-05-2011, 07:57 AM
Replies: 11
Views: 4,355
Posted By brachysclereid
Idease on q scores

Thanks!

I used the biopython suggestion and now have the .qual files. This is what I wanted.

kwyattm,
Is there a tool that will take a random sample of the .qual file in R for the purpose...
Forum: Bioinformatics 12-04-2011, 04:45 PM
Replies: 11
Views: 4,355
Posted By brachysclereid
Ideas on collecting quality scores per base in an illumina fastq file

Hi,

I am trying to make per base quality plots like fastqc because I would like to customize reporting. The summary stats reported by fastq in the text export is difficult to work with in R....
Forum: Bioinformatics 09-29-2011, 08:42 AM
Replies: 1
Views: 2,125
Posted By brachysclereid
Cufflinks, Cuffdiff, without replicates

Hi,

Can anyone help to understand how cufflinks/cuffdiff functions in the absence of replicates in layman's terms? I have read the website a few times and I'm afraid that I am missing...
Forum: Bioinformatics 08-31-2011, 07:09 AM
Replies: 5
Views: 2,666
Posted By brachysclereid
csfasta to fasta

I would still like to do this. In theory those problems would result in kmers occurring only once or a few times in the data set and could be removed.


Does such a script exist?
Forum: Bioinformatics 08-30-2011, 08:14 PM
Replies: 5
Views: 2,666
Posted By brachysclereid
csfasta to fasta?

Is anyone aware of a script that will convert a color space fasta to a fasta file?
Forum: Bioinformatics 06-09-2011, 01:12 PM
Replies: 4
Views: 3,676
Posted By brachysclereid
de Bruijn

I did try that and was unable to turn anything up. I did find this geeky shrine to de Bruijn: http://chessprogramming.wikispaces.com/Nicolaas+de+Bruijn

They have several of his works available as...
Forum: Bioinformatics 06-09-2011, 01:02 PM
Replies: 4
Views: 3,676
Posted By brachysclereid
De Bruijn, N. G. (1946). A Combinatorial Problem. Koninklijke Nederlandse Akademie v.

Does anyone have a PDF copy of the following paper? I see it cited frequently, but I am unable to locate it myself.

De Bruijn, N. G. (1946). A Combinatorial Problem. Koninklijke Nederlandse...
Forum: Bioinformatics 05-19-2011, 08:00 PM
Replies: 3
Views: 3,155
Posted By brachysclereid
Finding Exon-Intron Junctions without a reference genome

Thanks for the advice. I'll try using a relative.
Forum: Bioinformatics 05-19-2011, 12:52 PM
Replies: 3
Views: 3,155
Posted By brachysclereid
Finding Exon-Intron Junctions without a reference genome

Hi,
I'm trying to find intron-exon junctions in assembled transcriptome data without a reference genome. Does anyone know of a tool that can do this?
Forum: Bioinformatics 05-03-2011, 06:31 PM
Replies: 2
Views: 6,751
Posted By brachysclereid
Thanks Nils. I went with the 3.4GHz i7. Sounds...

Thanks Nils. I went with the 3.4GHz i7. Sounds sweet.
Forum: Bioinformatics 05-03-2011, 10:10 AM
Replies: 2
Views: 6,751
Posted By brachysclereid
3.4GHz Quad-Core Intel Core i7 versus 3.1GHz Quad-Core Intel Core i5

Hi,
I am looking at buying some iMAC workstations for our lab. We can access larger linux computing resources for big jobs, but this for basic stuff such as alignments & RNAseq (we work with...
Forum: Bioinformatics 02-28-2011, 06:58 AM
Replies: 10
Views: 5,085
Posted By brachysclereid
cufflinks version 1.0

Thanks for the information. Did they mention when they would release that version?
Forum: Bioinformatics 02-26-2011, 01:57 PM
Replies: 2
Views: 1,384
Posted By brachysclereid
RNA-seq(tophat|cufflinks) on part of a genome: special considerations?

Hi,
I was wondering if there are any particular considerations one must take into account when running RNA-seq on just a small part of the genome. Such as areas surrounding a few GWAS hits?
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