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User: Niek De Klein

gravatar for Niek De Klein
Niek De Klein • 2.4k
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Netherlands
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Joined:
8 years ago
Email:
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4th year bioinformatics student

Posts by Niek De Klein

<prev • 248 results • page 1 of 25 • next >
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Comment: C: How to convert fastq to cram, and from cram back to fastq
... I made a stupid mistake, was counting lines of the gzipped fastq file and comparing to an unzipped fastq file. After fixing that there was still a small difference, as STAR by default doesn't put unmapped reads in the output file, so had to --outSAMunmapped Within option. After that I got the corr ...
written 15 days ago by Niek De Klein • 2.4k
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Comment: C: How to convert fastq to cram, and from cram back to fastq
... Thanks, I'm testing this now and seeing how it compares to removing secondary aligned reads ...
written 22 days ago by Niek De Klein • 2.4k
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How to convert fastq to cram, and from cram back to fastq
... I want to save my fastq files as CRAM files to save space. However, I do want to be able to get the reads back that I have in my fastq, in case I have to reallign in a different way in the future. Below I have the code that I use to do the conversions to BAM and back again. However, when I then chec ...
fastq cram written 23 days ago by Niek De Klein • 2.4k • updated 22 days ago by finswimmer ♦ 5.3k
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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 12 months ago by Niek De Klein • 2.4k • updated 12 months ago by Pierre Lindenbaum ♦ 112k
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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 13 months ago by Niek De Klein • 2.4k
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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 13 months ago by Niek De Klein • 2.4k
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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 13 months ago by Niek De Klein • 2.4k • updated 13 months ago by Alex Reynolds ♦ 25k
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Comment: C: Extremely low assigned reads in featureCounts
... Was the sequencing done strand-specific? ...
written 14 months 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 22 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 22 months ago by Niek De Klein • 2.4k

Latest awards to Niek De Klein

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Epic Question 2.6 years 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?
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Prophet 2.8 years ago, created a post with more than 20 followers. For What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
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