Moderator: Leszek

gravatar for Leszek
Leszek3.6k
Reputation:
3,640
Status:
Trusted
Location:
IIMCB, Poland
Website:
http://bioinfoexpert.com/
Twitter:
lpryszcz
Scholar ID:
Google Scholar Page
Last seen:
5 days, 6 hours ago
Joined:
6 years, 4 months ago
Email:
l**********@gmail.com

I’m bioinformatician with background in molecular biology and biotechnology fascinated by technological developments. Recently, I’m actively working with Next-Generation Sequencing (NGS) data.

Posts by Leszek

<prev • 294 results • page 1 of 30 • next >
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Comment: C: Recommendations For Heterozygous Genome Assembly Software
... you need to add the path to GapCloser to your system PATH. Have a look how to do it: https://github.com/lpryszcz/redundans/issues/23 ...
written 4 months ago by Leszek3.6k
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Job: A bioinformatics specialist position at IIMCB, Warsaw, Poland
... IIMCB (http://iimcb.gov.pl) is the top-ranked Polish research institute in the field of biology. The institute provides cutting-edge equipment and facilities, Illumina Nextseq500, strong computational cluster, and a fully functional zebrafish facility. IIMCB is committed to provide a supportive and ...
poland bioinformatics ngs job warsaw written 8 months ago by Leszek3.6k
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Comment: C: Prague Summer School - Next-Gen Seq Data Analysis 2016 (13 seats available)
... Slightly cheaper alternative, dedicated especially for young scientists from central Europe (V4 region): https://www.biostars.org/p/196803/ or http://ngschool.eu/ ...
written 9 months ago by Leszek3.6k
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News: Summer School in Bioinformatics & NGS Data Analysis
... I'd like to invite you to [**NGSchool2016: Summer School in Bioinformatics & NGS Data Analysis**][1] that will be held on **August 14-21, 2016 in [Dolný Smokovec, Slovakia][2]** ([High Tatras][3]). The course consists of series of lectures and hands-on workshops, covering various aspects of Co ...
dnaseq news summer shool ngs rnaseq chipseq written 9 months ago by Leszek3.6k
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Comment: C: Recommendations For Heterozygous Genome Assembly Software
... good point. we are involved in very challenging genomes (2-3Gb plants), but unfortunately for these challenging genomes there is no good reference to compare with... ...
written 12 months ago by Leszek3.6k
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Comment: C: Recommendations For Heterozygous Genome Assembly Software
... the gaps can be filled ie using GapCloser, removing most of Ns from the assembly ...
written 12 months ago by Leszek3.6k
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Comment: C: Recommendations For Heterozygous Genome Assembly Software
... Yes, reduction step will remove contigs representing highly similar repeats. but if you have mate pair libraries you will recover these missing regions during scaffolding step. From simulations with *A. thaliana* genome (~25% of which is repeats) I've observed reduction of the assembly to ~80-90% o ...
written 12 months ago by Leszek3.6k
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Comment: C: Nextseq for analysts
... We are also using NextSeq + BaseSpace onsite. Lately, we've reconfigured it to dump raw data to NFS. I'd like to process it in the cluster, but I don't see `SampleSheet.csv` in main run directory and anywhere else. Any idea where it is?  ...
written 14 months ago by Leszek3.6k
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Comment: C: Python-friendly tools for RNA secondary structure visualisation & manipulation
... Thanks Ryan, that's really good hint! Actually I've found it in meantime :) I cannot find the option to generate the structure images, but I'll do some stats with forgi at least :D ...
written 19 months ago by Leszek3.6k
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Python-friendly tools for RNA secondary structure visualisation & manipulation
... I'm looking for Python tools (or tools with Python bindings) for manipulation and visualisation of RNA secondary structures. In principle, I would like to annotate (maybe with colours) some of the bases from 2D structures.   Can you recommend me some solutions?   ...
python visualisation secondary structure rna written 19 months ago by Leszek3.6k • updated 19 months ago by Ryan Dale4.4k

Latest awards to Leszek

Scholar 5 weeks ago, created an answer that has been accepted. For A: What are the best approaches to evaluate a genome assembly using the 'intrinsic'
Appreciated 3 months ago, created a post with more than 5 votes. For A: Scaffolding: Is This Legit?
Popular Question 3 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Phylogenetic Trees
Popular Question 4 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Appreciated 5 months ago, created a post with more than 5 votes. For A: Scaffolding: Is This Legit?
Great Question 6 months ago, created a question with more than 5,000 views. For Plotting Density Of Snps On Chromosomes
Great Question 6 months ago, created a question with more than 5,000 views. For Genbank To Gtf Converter
Popular Question 6 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Great Question 7 months ago, created a question with more than 5,000 views. For Genbank To Gtf Converter
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Recommendations For Heterozygous Genome Assembly Software
Popular Question 8 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Popular Question 8 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Popular Question 9 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Prophet 9 months ago, created a post with more than 20 followers. For Recommendations For Heterozygous Genome Assembly Software
Great Question 9 months ago, created a question with more than 5,000 views. For Plotting Density Of Snps On Chromosomes
Popular Question 10 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Appreciated 11 months ago, created a post with more than 5 votes. For A: Scaffolding: Is This Legit?
Popular Question 12 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Prophet 12 months ago, created a post with more than 20 followers. For Recommendations For Heterozygous Genome Assembly Software
Appreciated 13 months ago, created a post with more than 5 votes. For A: Scaffolding: Is This Legit?
Popular Question 13 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data
Scholar 13 months ago, created an answer that has been accepted. For A: What are the best approaches to evaluate a genome assembly using the 'intrinsic'
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Scaffolding: Is This Legit?
Popular Question 13 months ago, created a question with more than 1,000 views. For How To Find Stranded Rna-Seq Experiments Data

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