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Forum: Illumina/Solexa 02-23-2016, 12:31 PM
Replies: 1
Views: 1,920
Posted By amango
Index sequencing primer for use with custom primers (16S metagenomic)

I'm trying to determine the correct index sequencing primer to use with a set of custom primers designed to amplify a locus (16S rDNA) while also adding adapters (for Illumina Miseq) and index...
Forum: Bioinformatics 09-24-2012, 10:23 AM
Replies: 8
Views: 5,422
Posted By amango
Alex, did you ever find a solution to this? If so...

Alex, did you ever find a solution to this? If so would you mind sharing? I have the exact some problem, and I am also a beginner. I used tblastn to compare my own de novo assembled contigs to a...
Forum: Bioinformatics 09-01-2012, 06:36 AM
Replies: 1
Views: 2,273
Posted By amango
extracting predicted gene from scaffold: end position precedes start position

I am trying to extract sequences for a list of predicted genes from genomic scaffolds. The list of predicted genes with Scaffold IDs, start and end positions, and other info comes from published...
Forum: Bioinformatics 07-19-2012, 07:22 AM
Replies: 6
Views: 5,354
Posted By amango
You've probably already figured this out, but the...

You've probably already figured this out, but the Trinity documentation describes what you should do:

http://trinityrnaseq.sourceforge.net/#running_trinity

If you have both paired and unpaired...
Forum: Bioinformatics 07-16-2012, 07:23 AM
Replies: 17
Views: 9,940
Posted By amango
I have used Abyss and then Trans-abyss for a de...

I have used Abyss and then Trans-abyss for a de novo transcriptome assembly with ~70 million reads on a machine with 20gb RAM. From what I've read Abyss is less RAM-intensive than other Trinity and...
Forum: RNA Sequencing 05-22-2012, 08:30 AM
Replies: 5
Views: 2,726
Posted By amango
Were you ever able to resolve this? I am having...

Were you ever able to resolve this? I am having the same problem. Using blastx on my de novo assembly against the NCBI nr database (pre-formatted) yields an empty output file. When I run the same...
Forum: Bioinformatics 03-02-2012, 09:37 AM
Replies: 10
Views: 9,700
Posted By amango
Line 60897629 is indeed different. It's the...

Line 60897629 is indeed different. It's the middle one below, starting with "165...". I looked a hundred lines before this section, and it seems to be the first that appears this way, the some other...
Forum: Bioinformatics 03-02-2012, 07:30 AM
Replies: 10
Views: 9,700
Posted By amango
SAM (from bowtie2) to BAM problem using samtools

I generated a de novo assembly of illumina hiseq reads using Abyss & trans-Abyss, aligned the reads back to the assembly using bowtie2, and am now trying to view the resulting SAM alignment in IGV....
Forum: Bioinformatics 02-04-2012, 01:53 PM
Replies: 9
Views: 7,947
Posted By amango
I did re-run trimmomatic on my fastq files, this...

I did re-run trimmomatic on my fastq files, this time specifying --phred33, and it seems to have worked.

However, when I tried to assess the resulting output files using fastQC, I run into...
Forum: Bioinformatics 02-03-2012, 06:59 AM
Replies: 9
Views: 7,947
Posted By amango
Thanks for the input. I received another tip that...

Thanks for the input. I received another tip that since my data was generated on a Hiseq, quality scores are probably phred33, whereas the Trimmomatic default is phred64. I will specify phredd33 and...
Forum: Bioinformatics 02-02-2012, 12:36 PM
Replies: 9
Views: 7,947
Posted By amango
Problem with trimmomatic

I ran trimmomatic on my 100bp paired end Illumina hiseq dataset using the command below. But the output files were all empty when unzipped (4kb when zipped). The program ran for around 8 hours (each...
Forum: Bioinformatics 01-30-2012, 08:39 PM
Replies: 4
Views: 6,284
Posted By amango
Source of duplication in illumina hiseq paired-end reads?

I recently received my first short read data set, one lane of 2x100bp Illumina Hiseq reads. I'm hoping the community can help me identify the source of duplicate sequences indicated in fastQC reports...
Forum: Illumina/Solexa 09-13-2011, 09:07 PM
Replies: 0
Views: 2,305
Posted By amango
estimating sequencing coverage for multiplexed mrna-seq

I am planning a library construction approach for one lane of 100nt paired end Hiseq sequencing. It's a (non-model) population-level study so I'll need to multiplex. I'm hoping to get some...
Forum: Sample Prep / Library Generation 04-15-2011, 05:00 PM
Replies: 7
Views: 4,410
Posted By amango
These authors published a protocol for exactly...

These authors published a protocol for exactly what you seek to do:
Yoon and Brem. Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA (2010) vol. 16 (6) pp....
Forum: Illumina/Solexa 01-11-2011, 12:28 PM
Replies: 8
Views: 3,752
Posted By amango
problems with indexed paired-end mRNA-seq

JMorlan, gford, josdegraaf and anyone else,
I am working on a 'homemade' paired-end indexed mRNA-seq protocol. I am having trouble amplifying my adapter-ligated library (or maybe I'm having trouble...
Forum: Illumina/Solexa 05-12-2010, 01:09 PM
Replies: 145
Views: 317,075
Posted By amango
I noticed that several people were wondering...

I noticed that several people were wondering about adaptor and primer concentrations in the Illumina kit. I just spoke to an Illumina tech support person, and for RNA-seq at least, the working...
Forum: Illumina/Solexa 05-07-2010, 06:52 AM
Replies: 4
Views: 2,619
Posted By amango
unexpected cDNA product during library prep

Attached are Bioanalyzer traces from various points in my illumina library preparation protocol for RNA-seq, modified to sequence only 3 transcript ends. Graphs are from different samples since...
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