Analysis of DNA, RNA or protein (amino acid) sequences. Here sequences are compared so analyze similarities and conserved regions. Sequence analysis is usually done by specialized software.

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What do Illumina HiSeq/MiSeq paired end reads look like?

My understanding is that paired end reads from the Illumina HiSeq/MiSeq platforms looks something like this: R1: AAAAAACCCCCC R2: GGGGGGTTTTTT Where the ...
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62 views

Standard practice for generating rarefaction curves from Next Generation Sequencing data

We have a few million 18S reads from a particular environment. The reads have been clustered into Operational Taxonomic Unit (OTU), and the OTUs annotated against a reference database. To generate a ...
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How can I create R8 (homopolymer repeat) filter without using illumina pipeline?

illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and ...
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136 views

Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have ...
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Efficient algorithm to calculate various population divergence statistics

Intro and description of the data I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format ...
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What is the sequence of pPROLar.A plasmid?

I've been looking for the sequence of pPROLar.A122 plasmid but I haven't found it. Where could I find the sequence? The first link (addgene) on googling reports a plasmid which is reported to have ...
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23 views

Batch several sequences for absent restriction sites

I have a collection of about 120 7kB sequences I would like to check for ether a list of specific restriction sites, or what restriction sites might be absent in all of them. Is there a app or ...
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28 views

Genotype-Phenotype databases?

Beyond the Stanford HIV database, what other databases out there provide a dataset linking virus/bacterial genotype to quantitative phenotype? I'm looking for high quality datasets to test machine ...
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42 views

What are constrained genetic elements?

I am somewhat of a newbie in evolutionary biology currently taking my first steps in bioinformatics. I was reading a paper when I came across the term "constrained genetic elements", referring to ...
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186 views

Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?

I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this ...
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Which ScoreMatrix and GapPenalties should I use?

I'm a Software Engineering student, and I'm dealing with a Sequence Analysis problem. The problem is the following: Find phenylalanine hydroxylase of at least six different species, then perform a ...
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24 views

Walkthrough Analyzing/Processing Genotyping Data for Association Studies

I need help outlining the data analysis process of analyzing genotyping data you get back from a Next Generation Sequencing experiment. Here are the steps I currently believe you go through, but I ...
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How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
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Why low variant frequency in exomeseq data (ANNOVAR)?

I've got an annotated ANNOVAR file with 300.000 nucleotide variants of 4 genomes. There's one thing I don't understand when looking at the data: Why are the variant frequencies so low in comparison to ...
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68 views

Demultiplexing symmetric PacBio reads

I have PacBio CCS.h5 and the corresponding fasta and fastq files and I would like to demultiplex them. Does anyone know of how this can be done in the absence of bas.h5 files. Thanks for your help! ...