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User: Niek De Klein

gravatar for Niek De Klein
Niek De Klein • 2.4k
Reputation:
2,350
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Trusted
Location:
Netherlands
Website:
http://-
Last seen:
14 hours ago
Joined:
6 years, 10 months ago
Email:
n**********@gmail.com

4th year bioinformatics student

Posts by Niek De Klein

<prev • 242 results • page 1 of 25 • next >
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Comment: C: Extremely low assigned reads in featureCounts
... Was the sequencing done strand-specific? ...
written 24 days ago by Niek De Klein • 2.4k
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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 8 months ago by Niek De Klein • 2.4k
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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 8 months ago by Niek De Klein • 2.4k
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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 8 months ago by Niek De Klein • 2.4k
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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 9 months ago by Niek De Klein • 2.4k
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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 9 months ago by Niek De Klein • 2.4k
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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 9 months ago by Niek De Klein • 2.4k
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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 12 months ago by Niek De Klein • 2.4k • updated 12 months ago by WouterDeCoster ♦ 20k
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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 20 months ago by Niek De Klein • 2.4k • updated 20 months ago by 5heikki ♦ 6.5k
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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 21 months ago by Niek De Klein • 2.4k • updated 21 months ago by Emily_Ensembl ♦ 12k

Latest awards to Niek De Klein

Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to remove non-unique mapping reads with Hisat?
Scholar 8 months ago, created an answer that has been accepted. For A: How To Install The Ucsc In The Linux Operating System
Popular Question 8 months ago, created a question with more than 1,000 views. For Biopython Ncbistandalone Blastall Gives Different Result Than Calling Blastall Directly From Cmd
Popular Question 8 months ago, created a question with more than 1,000 views. For What Is (Or How To Find Out) The Meaning Of Error Code -1073741510 From Local Blast 2.2.25+?
Popular Question 8 months ago, created a question with more than 1,000 views. For How To Show More Blast Results Using Biopython?
Popular Question 8 months ago, created a question with more than 1,000 views. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Prophet 8 months ago, created a post with more than 20 followers. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Popular Question 9 months ago, created a question with more than 1,000 views. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Why Gene Regulatory Network Is Sparse？
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Popular Question 12 months ago, created a question with more than 1,000 views. For How To Show More Blast Results Using Biopython?
Popular Question 14 months ago, created a question with more than 1,000 views. For Windows Cmd Not Responding With Python Blastall 2.2.17
Popular Question 14 months ago, created a question with more than 1,000 views. For When To Choose Python Over Perl (And Vice Versa)?
Popular Question 17 months ago, created a question with more than 1,000 views. For How To Convert .Mgf (Mascot Generic File) To A Format (Mzxml?) So That They Can Be Used With Maxquant?
Student 17 months ago, asked a question with at least 3 up-votes. For How To Convert .Mgf (Mascot Generic File) To A Format (Mzxml?) So That They Can Be Used With Maxquant?
Epic Question 17 months ago, created a question with more than 10,000 views. For When Using Heatmap.2 From R To Make A Heatmap Of Microarray Data, How Are The Genes Clustered?
Prophet 20 months ago, created a post with more than 20 followers. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Student 24 months ago, asked a question with at least 3 up-votes. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Biopython Ncbistandalone Blastall Gives Different Result Than Calling Blastall Directly From Cmd
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Is Conversion From Colorspace To Base Space Lossy?
Great Question 2.2 years ago, created a question with more than 5,000 views. For When To Choose Python Over Perl (And Vice Versa)?
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Epigenetics
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: How To Install The Ucsc In The Linux Operating System
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