User: Niek De Klein

gravatar for Niek De Klein
Niek De Klein2.3k
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Netherlands
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Last seen:
6 months ago
Joined:
6 years, 8 months ago
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4th year bioinformatics student

Posts by Niek De Klein

<prev • 241 results • page 1 of 25 • next >
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Answer: A: Shapeit can't open existing file
... Don't know how to delete the question, but turns out `chr1.sample` does not exist, the error was just showing the wrong file. ...
written 6 months ago by Niek De Klein2.3k
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Comment: C: Shapeit can't open existing file
... chr_1.haps.gz: gzip compressed data, was "chr_1.haps", from Unix, last modified: Wed Feb 24 16:13:24 2016 ...
written 6 months ago by Niek De Klein2.3k
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(Closed) Shapeit can't open existing file
... I am trying to run Shapeit -call function. However, it gives me the error `chr_1.haps.gz is impossible to open, check file existence or reading permissions`. I have set the file permissions completely open and checked that the file exists: `ll chr_1.haps.gz` `-rwxrwxrwx 1 ndeklein group 8694707 Nov ...
shapeit written 6 months ago by Niek De Klein2.3k
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Comment: C: How to add info to the sample columns of a VCF?
... Yes, saw my mistake and edited it ...
written 7 months ago by Niek De Klein2.3k
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Comment: C: How to add info to the sample columns of a VCF?
... I have a tab delimited file sample_name snp CHR SNP pos value but I can put it in a different format. ...
written 7 months ago by Niek De Klein2.3k
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How to add info to the sample columns of a VCF?
... Is there a tool that can add information to the sample columns of a VCF file, similar to bcftools --annotations but instead of changing the INFO column the FORMAT column + all the sample information? So if I have the line 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 ...
vcf bcftools written 7 months ago by Niek De Klein2.3k
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Hisat R strandness aligning same strand as F strandness, how to do it correctly?
... I have RNA-sequence data where the RNA was isolated using the ribo-zero protocol. I (presumably) have the reverse complement of the transcript. I aligned them using Hisat2 with ``` hisat2 -x index -U input.fastq -S output.sam --rna-strandness R ``` However, when viewing it in IGV the reads are al ...
hisat2 alignment strandness rna-seq ribo-zero written 10 months ago by Niek De Klein2.3k • updated 10 months ago by WouterDeCoster17k
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Recognize rRNA remove protocol from gene expression profile
... We have a large amount of samples for which we don't know the protocol that was used to extract the RNA. We want to know which samples were processed using the Poly-A selection protocol, and which with the Ribo-Zero-Seq protocol. Is there a tool available that can do this? ...
ribozero rna-seq poly-a written 18 months ago by Niek De Klein2.3k • updated 18 months ago by 5heikki6.3k
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biomaRt LPR region to position giving different results than I expect (using R)
... I am trying to map some ensembl gene IDs and LRG regions to position on the genome. I got the gene IDs and LRG regions by mapping transcript IDs to gene IDs with mapping <- getBM(attributes = c("ensembl_transcript_id","ensembl_gene_id","hgnc_symbol",'chromosome_name','start_position','end_posit ...
ensembl biomart written 19 months ago by Niek De Klein2.3k • updated 19 months ago by Emily_Ensembl11k
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Showing both strands in IGV, or if not possible what genome viewer is good for strand specific experiments?
... I have strand specific RNA seq data that I would like to view in IGV or a similar genome browser (with fast scrolling/zooming). I am looking for something like the (a) part of this figure (from RNASeqBrowser): Where the positive strand is above the line, and negative strand is below the line. At t ...
genome-browser igv written 20 months ago by Niek De Klein2.3k • updated 20 months ago by Zaag530

Latest awards to Niek De Klein

Popular Question 7 months ago, created a question with more than 1,000 views. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Popular Question 10 months ago, created a question with more than 1,000 views. For How To Show More Blast Results Using Biopython?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Why Gene Regulatory Network Is Sparse?
Popular Question 12 months ago, created a question with more than 1,000 views. For Windows Cmd Not Responding With Python Blastall 2.2.17
Popular Question 12 months ago, created a question with more than 1,000 views. For When To Choose Python Over Perl (And Vice Versa)?
Prophet 18 months ago, created a post with more than 20 followers. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Student 22 months ago, asked a question with at least 3 up-votes. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Great Question 2.0 years ago, created a question with more than 5,000 views. For When To Choose Python Over Perl (And Vice Versa)?
Good Answer 2.0 years ago, created an answer that was upvoted at least 5 times. For A: Epigenetics
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: How To Install The Ucsc In The Linux Operating System
Good Question 2.0 years ago, asked a question that was upvoted at least 5 times. For When To Choose Python Over Perl (And Vice Versa)?
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Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Blast Results: Xml Tags Explained ?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: How Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
Student 3.3 years ago, asked a question with at least 3 up-votes. For How Can I Get The Retention Time Of An Ms/Ms Precursor Out Of A Mzml File Using Pymzml?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: How Do You Manage Your Files & Directories For Your Projects ?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: C Programing In Bioinformatics
Student 3.3 years ago, asked a question with at least 3 up-votes. For Program Or Script To Go From Partial Protein Sequence To Dna

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