User: Alex

gravatar for Alex
Alex1.4k
Reputation:
1,450
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Location:
Theodosius Dobzhansky Center for Genome Bioinformatics
Last seen:
1 year, 3 months ago
Joined:
9 years, 7 months ago
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Posts by Alex

<prev • 51 results • page 1 of 6 • next >
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Any state of the art tool for reads generation from reference sequence?
... Dear Biostar Community, What is the best tool for read generation from given reference sequences or any that you use/used and it works/worked as expected? The properties of desired tool: - reads generate of given insert size and read length with uniform coverage - handle uniform coverage on circ ...
illumina reads generation pacbio reads simulation written 3.5 years ago by Alex1.4k
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PacBio transcriptome and gene annotation
... I have: 1) well assembled PacBio only genome with related organism with well annotated genes 2) Illumina transcriptome 3) PacBio transcriptome 4) Not so good as expected genes annotation with Maker and Illumina transcriptome Do you try use PacBio transcriptome for gene annotation with Maker or ...
genes maker pacbio transcriptome written 4.7 years ago by Alex1.4k • updated 4.7 years ago by Biostar ♦♦ 20
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Comment: C: mDust location for running MITE-Hunter
... Karl, finally I used dust from NCBI blast package and it works well and returns same format as mDUST ...
written 4.8 years ago by Alex1.4k
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SMART libraries for InterProScan
... I'm trying to install interproscan-5.8-49.0 and I don't know where I can find SMART overlapping and threshold libraries for: # Note: Smart overlapping and threshold files not distributed with InterProScan 5, please install separately e.g. in data/smart/6.2 smart.hmm.path.6.2=data/smart/6.2/smart. ...
smart interproscan missing libraries written 4.8 years ago by Alex1.4k • updated 4.3 years ago by ganga.jeena30
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mDust location for running MITE-Hunter
... Where I can find mDust program? I need it for running MITE-Hunter (http://target.iplantcollaborative.org/mite_hunter/MITE-Hunter_manual.pdf), all links from google broken and Celera deleted mDust page. May be someone has it and can share it? Or ff you know how to run MITE-Hunter without mDust it wi ...
mdust old soft mite-hunter written 5.0 years ago by Alex1.4k • updated 8 months ago by ohon.kin0
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The fastest way to check read orientation for mate pair library
... I have a lot of mate pair libraries with unknown reads orientation. What is the current fastest way to determine it? As some additional complication: some libraries don't have reference genome for mapping.  ...
illumina reads orientation mate pair written 5.2 years ago by Alex1.4k
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Any high quality mouse dataset for k-mer counting?
... Do you know any high quality Illumina dataset with minimal biases and high coverage for mouse genome? Something likes Illumina Platinum genomes for human genome. There is one from ALLPATH-LG paper but it is probably too old. ...
dataset hiseq mouse illumina written 5.3 years ago by Alex1.4k • updated 3.5 years ago by Biostar ♦♦ 20
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Seedmasker documentation or usage example
... Hi everyone, Does anyone have any experience with seedmasker (http://www.drive5.com/seedmasker/)? Any manual or usage example? ...
seedmasker masking repeats msa written 5.3 years ago by Alex1.4k
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Comment: C: Edgeredef Failed When Running Repeatmodeler
... Same error, any ideas? ...
written 5.7 years ago by Alex1.4k
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Customize Link To Ncbi Blast Search
... I want to insert a link to NCBI Blast search into web page with given GI and coordinates. Link like this: <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&QUERY={{ GI }}&DATABASE=nr&MEGABLAST=on&BLAST_PROGRAMS=megaBlast&LINK_LOC=nuccore& ...
ncbi blast written 6.2 years ago by Alex1.4k • updated 6.2 years ago by Istvan Albert ♦♦ 81k

Latest awards to Alex

Popular Question 2.0 years ago, created a question with more than 1,000 views. For The fastest way to check read orientation for mate pair library
Popular Question 2.1 years ago, created a question with more than 1,000 views. For mDust location for running MITE-Hunter
Great Question 2.9 years ago, created a question with more than 5,000 views. For Huge Tree Visualization
Popular Question 2.9 years ago, created a question with more than 1,000 views. For mDust location for running MITE-Hunter
Popular Question 2.9 years ago, created a question with more than 1,000 views. For The fastest way to check read orientation for mate pair library
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Best Way To Map Sra Data To 100Kb Dna Fragment
Student 3.5 years ago, asked a question with at least 3 up-votes. For Huge Tree Visualization
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Gff3 Format - Human Genome
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Tool/Library For Drawing Nice Synteny Map
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Popular Question 4.2 years ago, created a question with more than 1,000 views. For Huge Tree Visualization
Student 4.6 years ago, asked a question with at least 3 up-votes. For Huge Tree Visualization
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Ideogram Mapview Data For Human Genome Build 37.2
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Huge Tree Visualization
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Gff3 Format - Human Genome
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Using Amazon Web Services?
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: List Of Completed Genome Projects And Metagenomics Projects
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Getting List Of Pmcids From Pubmed Central
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: How To Fetch Genomics Sequence Using Coordinates In Biopython
Appreciated 5.7 years ago, created a post with more than 5 votes. For Huge Tree Visualization
Appreciated 5.7 years ago, created a post with more than 5 votes. For How Many Human Genome Assemblies Are Avaliable?
Good Question 5.7 years ago, asked a question that was upvoted at least 5 times. For Huge Tree Visualization
Good Question 5.7 years ago, asked a question that was upvoted at least 5 times. For How Many Human Genome Assemblies Are Avaliable?
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Gff3 Format - Human Genome
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Using Amazon Web Services?

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