User: Niek De Klein

gravatar for Niek De Klein
Niek De Klein2.4k
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4th year bioinformatics student

Posts by Niek De Klein

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GaTK reverse select interval list
... 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_ ...
gatk intervallist written 10 weeks ago by Niek De Klein2.4k • updated 10 weeks ago by Pierre Lindenbaum100k
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Comment: C: Bedtools merge only part of feature that overlaps, not whole feature
... 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 3 months ago by Niek De Klein2.4k
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Answer: A: Get sequences from oligonucleotide probe ids
... 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 3 months ago by Niek De Klein2.4k
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Bedtools merge only part of feature that overlaps, not whole feature
... 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 . - ...
bedtools bed merge written 3 months ago by Niek De Klein2.4k • updated 3 months ago by Alex Reynolds21k
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Comment: C: Extremely low assigned reads in featureCounts
... Was the sequencing done strand-specific? ...
written 4 months ago by Niek De Klein2.4k
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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 11 months ago by Niek De Klein2.4k
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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 11 months ago by Niek De Klein2.4k
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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 11 months ago by Niek De Klein2.4k
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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 12 months ago by Niek De Klein2.4k
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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 12 months ago by Niek De Klein2.4k

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Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Epigenetics

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