User: j.matt.franklin

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Posts by j.matt.franklin

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Comment: C: find unique sequences among a set of fasta entries
... Thanks! This is helpful. ...
written 2 days ago by j.matt.franklin0
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find unique sequences among a set of fasta entries
... What is the best way to determine arbitrary-length uniqueness for sequences? Let's say I have 100 DNA sequences, ranging from 300bp to 100kb. I want to know all the regions of each sequence that is unique among this set. The individual sequences contain significant repeat DNA, so I want to know wh ...
genome repeat alignment blast written 3 days ago by j.matt.franklin0 • updated 3 days ago by Mensur Dlakic9.1k
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Comment: A: Help with analyzing NCBI tissue expression data - solr xml file
... Wow that worked perfectly! Thanks. ...
written 9 days ago by j.matt.franklin0
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Help with analyzing NCBI tissue expression data - solr xml file
... I'm trying to access the complete ncbi tissue expression dataset. When you look at any individual gene, NCBI provides a expression chart to look at rna-seq counts across tissues. For example, https://www.ncbi.nlm.nih.gov/gene/6304 You can see higher expression in brain and lymph nodes. I contact ...
ncbi tissue expression solr rna-seq xml written 9 days ago by j.matt.franklin0
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How to annotate human genome?
... I am trying to annotate a human genome. There's some recent papers that have assembled the human genome from long-read sequencing. I can get the assembly from NCBI. There's a provided gbff file, but it doesn't include annotations of the actual human genes. What's the most standard way for me to ...
genome annotate written 12 weeks ago by j.matt.franklin0
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local galaxy Trackster can't find bedtools
... Hi I'm running galaxy locally. I am trying to get the Trackster visualization tool to work. The installation instructions are posted here: https://galaxyproject.org/visualization-setup/ When I attempt to run Trackster, I receive and error that bedtools cannot be found: PATH_TO_JOBS/tool_script.s ...
software error galaxy rna-seq written 3 months ago by j.matt.franklin0 • updated 3 months ago by Biostar ♦♦ 20
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Align chip seq data to specific sequences not in reference genome
... Hi all, I'm very new to bio-informatics, but have many years of coding experience. I am studying un-referenced parts of the genome. I.e. satellite repeats which aren't included in reference genomes. I want to align some raw chip seq data to some specific set of sequences. Basically, I want to make ...
alignment chip-seq written 7 months ago by j.matt.franklin0 • updated 6 months ago by Biostar ♦♦ 20

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