User: Ann

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Ann2.2k
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Location:
Concord NC USA
Website:
http://www.lorainelab....
Twitter:
aloraine205
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Last seen:
7 months, 1 week ago
Joined:
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Posts by Ann

<prev • 139 results • page 1 of 14 • next >
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what should a SAM/BAM record contain when there are no quality scores
... Hi! As everyone who works with this format already knows, the SAM/BAM sequence alignment format contains a field reserved for a per-base quality score string. But if per-base quality scores are not available, what value should this field contain? The specification (p. 16) says this field should c ...
bam samtools sam written 16 months ago by Ann2.2k • updated 16 months ago by jkbonfield40
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Job: Position available: Integrated Genome Browser Project, UNC-Charlotte, Charlotte, NC, USA
... Hello, The Integrated Genome Browser project has an opening! To apply, visit: - https://jobs.uncc.edu/postings/15721 For info, visit: - http://www.bioviz.org - Links to developer's guide, Jira, installers - http://www.bitbucket.org/lorainelab/integrated-genome-browser - Team code repository ...
java chip-seq igb rna-seq job written 19 months ago by Ann2.2k • updated 19 months ago by genomax59k
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Answer: A: PileOMeth double counting when paired-end reads overlap?
... Great news. I have been using this a lot - together with bwameth. Am getting very satisfying results. Thank you! As for names ... how about PileOBiseq ? Or BiseqTools? Where "biseq" is an abbreviation for "bisulfite" Seems like when you want to publish some software, reviewers will weigh in on ...
written 2.2 years ago by Ann2.2k
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PhD programs in bioinformatics and genomics
... Hello everyone, I am writing to ask your advice. I am looking for a list of Ph.D. programs in bioinformatics and genomics - ideally in the US. I am asking for a friend who is applying now but can start in just a few months - no need to wait until fall. What programs would you recommend? And of c ...
bioinformatics phd education written 2.2 years ago by Ann2.2k • updated 2.2 years ago by igor7.1k
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PileOMeth double counting when paired-end reads overlap?
... I'm using [PileOMeth][1] to create bedGraph-style files reporting the number of methylated and unmethylated bases at C positions in the genome. This is for a bisulfite sequencing experiment. My data are paired end. In many cases (but not all) reads from the same fragment overlap. This means that ...
methylation pileometh bisulfite written 2.2 years ago by Ann2.2k
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Comment: C: search datasets in IGB
... For accessing the ENCODE datasets, do you think we should take the data from the UCSC system or is there a better source? UCSC exposes their database for querying via interactive MySQL session and also allows computational access of that. In an email exchange with them, they said they were plannin ...
written 2.6 years ago by Ann2.2k
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Comment: C: Big Browser : a new genom browser in development
... Looks like you are using [overview-plus-detail][1] to implement jump-zooming to a new location. I think this is nice. UCSC, IGB, and many other genome browsers implement this same type of interaction. It's a great idea to re-use these conventions because then your interface will feel familiar to us ...
written 2.7 years ago by Ann2.2k
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Comment: C: Big Browser : a new genom browser in development
... And of course, handling chromosome synonyms, as Istvan mentioned in his comment, is one such key feature that is important to users. Handling chromosome and also genome version synonyms was one of the first features IGB users requested, back when it was developed at Affymetrix. To handle genome s ...
written 2.7 years ago by Ann2.2k
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Answer: A: Big Browser : a new genom browser in development
... Suggestion: Make sure to do due diligence - learn from other genome browsers. IGV is only one of many that have been developed by many groups - starting in 1988 with ACeDB. Genome browsers are essential tools in genomics. Anyone that deals with genomic data needs to visualize it. Developers in t ...
written 2.7 years ago by Ann2.2k
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need to identify CDS (translation) for gene models predicted by Cufflinks and Stringtie
... I have transcript models in GTF format made from assembling RNA-Seq read alignments using stringtie and also cufflinks. The reference genome is a new blueberry assembly I'm helping to annotate. For the next steps, I need to find the genomic coordinates of the start and end of translation for the lo ...
stringtie cufflinks rna-seq written 3.0 years ago by Ann2.2k • updated 3.0 years ago by Chirag Nepal2.1k

Latest awards to Ann

Popular Question 16 months ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 16 months ago, created a question with more than 1,000 views. For looking for plant ChIP-Seq data sets to try DiffBind (need replicates)
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: visualize tiling array file to IGB
Popular Question 16 months ago, created a question with more than 1,000 views. For tophat2 reported the same alignment twice for the same read (paired end data)
Popular Question 16 months ago, created a question with more than 1,000 views. For need to separate read1 and read2 to run tophat2
Popular Question 16 months ago, created a question with more than 1,000 views. For Please help support IGB software - need more letters of support
Popular Question 16 months ago, created a question with more than 1,000 views. For Integrated Genome Browser version 8.3 released - new native installer
Popular Question 16 months ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Popular Question 19 months ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 19 months ago, created a question with more than 1,000 views. For need to separate read1 and read2 to run tophat2
Popular Question 19 months ago, created a question with more than 1,000 views. For Integrated Genome Browser version 8.3 released - new native installer
Popular Question 24 months ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.6 years ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.7 years ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: how to use a bed file with htseq-count
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.9 years ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Student 3.0 years ago, asked a question with at least 3 up-votes. For how to use a bed file with htseq-count

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