User: Niek De Klein
Niek De Klein • 2.4k
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- Netherlands
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- Last seen:
- 16 hours ago
- Joined:
- 7 years, 7 months ago
- Email:
- n**********@gmail.com
4th year bioinformatics student
Posts by Niek De Klein
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2
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1
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325
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1
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... I have a file with RNA editing sites which I want to remove from my VCF. I can select all the RNA editing sites with:
java GenomeAnalysisTK.jar \
-T SelectVariants \
-R human_g1k_v37.fasta \
-V input.gg.vcf.gz \
-o output.gg.vcf.gz \
-L Human_AG_all_hg19_ ...
written 7 months ago by
Niek De Klein • 2.4k
• updated
7 months ago by
Pierre Lindenbaum ♦ 106k
0
votes
1
answer
477
views
1
answers
... Thanks for the detailed explanation! For others that find this question, this is how I went from ensemble GTF to BED with CHR, start, stop, ensemble gene ID:
awk '{if ($3 == "gene") print $0;}' Homo_sapiens.GRCh37.75.gtf \
| bedtools sort -i stdin \
| awk '{print $1 "\t" $4 "\t ...
written 8 months ago by
Niek De Klein • 2.4k
1
vote
2
answers
292
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2
answers
... The second column is an NCBI nucleotide ID, you can search the nucleotide database for the sequence. For example: https://www.ncbi.nlm.nih.gov/gquery/?term=XM_001122142.1 ...
written 8 months ago by
Niek De Klein • 2.4k
4
votes
1
answer
477
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1
answer
... I want to merge the genes in a bedfile so that only the parts of the gene that overlap become a new feature. E.g., have this bedfile:
1 pseudogene gene 11869 14412 . + . gene_id "ENSG00000223972"
1 pseudogene gene 14363 29806 . - ...
written 8 months ago by
Niek De Klein • 2.4k
• updated
8 months ago by
Alex Reynolds ♦ 23k
0
votes
0
answers
548
views
0
answers
... Was the sequencing done strand-specific? ...
written 9 months ago by
Niek De Klein • 2.4k
0
votes
1
answer
621
views
1
answers
... 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 17 months ago by
Niek De Klein • 2.4k
0
votes
1
answer
621
views
1
answers
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 17 months ago by
Niek De Klein • 2.4k
0
votes
1
answer
621
views
1
answer
... 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 ...
written 17 months ago by
Niek De Klein • 2.4k
0
votes
0
answers
724
views
0
answers
... Yes, saw my mistake and edited it ...
written 18 months ago by
Niek De Klein • 2.4k
0
votes
0
answers
724
views
0
answers
... I have a tab delimited file
sample_name snp CHR SNP pos value
but I can put it in a different format. ...
written 18 months ago by
Niek De Klein • 2.4k
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For How to remove non-unique mapping reads with Hisat?
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For A: How To Install The Ucsc In The Linux Operating System
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For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
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21 months ago,
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For A: Why Gene Regulatory Network Is Sparse？
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Is Conversion From Colorspace To Base Space Lossy?
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2.7 years ago,
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