Moderator: Leszek
Leszek ♦ 3.7k
- Reputation:
- 3,680
- Status:
- Trusted
- Location:
- IIMCB, Poland
- Website:
- http://bioinfoexpert.com/
- Twitter:
- lpryszcz
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 weeks, 4 days ago
- Joined:
- 6 years, 6 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
• 296 results •
page 1 of 30 •
next >
0
votes
10
answers
9.7k
views
10
answers
... you can post your questions regarding redundans / heterozygous genome assembly in https://groups.google.com/forum/#!forum/redundans
give more details, what is the species, expected genome size, what kind of libraries / assembler you are usings etc ...
written 9 weeks ago by
Leszek ♦ 3.7k
0
votes
15
answers
33k
views
15
answers
... cat file.fastq | python fastq_id_parser.py file_with_ids.txt > file_with_selected_ids.fastq ...
written 9 weeks ago by
Leszek ♦ 3.7k
0
votes
10
answers
9.7k
views
10
answers
... 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 7 months ago by
Leszek ♦ 3.7k
1
vote
0
answers
647
views
0
answers
... 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 ...
written 11 months ago by
Leszek ♦ 3.7k
0
votes
4
answers
3.0k
views
4
answers
... Slightly cheaper alternative, dedicated especially for young scientists from central Europe (V4 region): https://www.biostars.org/p/196803/ or http://ngschool.eu/ ...
written 12 months ago by
Leszek ♦ 3.7k
2
votes
0
answers
706
views
0
answers
... 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 ...
written 12 months ago by
Leszek ♦ 3.7k
0
votes
10
answers
9.7k
views
10
answers
... 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 14 months ago by
Leszek ♦ 3.7k
0
votes
10
answers
9.7k
views
10
answers
... the gaps can be filled ie using GapCloser, removing most of Ns from the assembly ...
written 14 months ago by
Leszek ♦ 3.7k
0
votes
10
answers
9.7k
views
10
answers
... 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 15 months ago by
Leszek ♦ 3.7k
0
votes
3
answers
6.8k
views
3
answers
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 17 months ago by
Leszek ♦ 3.7k
Latest awards to Leszek
Good Answer
10 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Phylogenetic Trees
Scholar
4 months ago,
created an answer that has been accepted.
For A: What are the best approaches to evaluate a genome assembly using the 'intrinsic'
Popular Question
6 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
Good Answer
7 months ago,
created an answer that was upvoted at least 5 times.
For A: Phylogenetic Trees
Popular Question
7 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
Great Question
9 months ago,
created a question with more than 5,000 views.
For Plotting Density Of Snps On Chromosomes
Great Question
9 months ago,
created a question with more than 5,000 views.
For Genbank To Gtf Converter
Popular Question
9 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
Great Question
10 months ago,
created a question with more than 5,000 views.
For Genbank To Gtf Converter
Good Question
10 months ago,
asked a question that was upvoted at least 5 times.
For Recommendations For Heterozygous Genome Assembly Software
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
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
Great Question
12 months ago,
created a question with more than 5,000 views.
For Plotting Density Of Snps On Chromosomes
Popular Question
12 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: Scaffolding: Is This Legit?
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
Prophet
15 months ago,
created a post with more than 20 followers.
For Recommendations For Heterozygous Genome Assembly Software
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: Scaffolding: Is This Legit?
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How To Find Stranded Rna-Seq Experiments Data
Scholar
16 months ago,
created an answer that has been accepted.
For A: What are the best approaches to evaluate a genome assembly using the 'intrinsic'
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 356 users visited in the last hour