User: Niek De Klein

gravatar for Niek De Klein
Niek De Klein2.5k
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Netherlands
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Posts by Niek De Klein

<prev • 253 results • page 1 of 26 • next >
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Comment: C: Code For Generating 'Consensus' Sequence From Pairwise Alignment
... Haven't tested for edge cases but can try something like this def consensus(*sequences): if(len(sequences) <= 1): raise RuntimeError('Only '+str(len(sequences))+' sequences given, need at least 2') consensus_sequence = '' for index, amino_acid in ...
written 8 months ago by Niek De Klein2.5k
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Comment: C: How can I fix picard error: Sequences at index 0 don't match
... The problem was in the .dict file, which was apparently made using the gzipped reference genome fasta, while the CRAM was made using the unzipped reference genome fasta. I remade the .dict file with the unzipped genome fasta file and now it works. Thanks for the help! ...
written 9 months ago by Niek De Klein2.5k
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Comment: C: How can I fix picard error: Sequences at index 0 don't match
... head -n30 /apps/data//ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_24/GRCh38.p5.genome.fa.fai chr1 248956422 8 60 61 chr2 242193529 253105712 60 61 chr3 198295559 499335808 60 61 chr4 190214555 700936301 60 61 chr5 181538259 894321107 60 61 chr6 170805979 10788 ...
written 9 months ago by Niek De Klein2.5k
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Comment: C: How can I fix picard error: Sequences at index 0 don't match
... Yes the path exists and the double / is not a problem. If the reference file can not be found it gives this error: `Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: /fake/path/genome.fa` ...
written 9 months ago by Niek De Klein2.5k
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How can I fix picard error: Sequences at index 0 don't match
... This is a cross-post from here: https://gatkforums.broadinstitute.org/gatk/discussion/13395/sequences-at-index-0-dont-match-but-using-the-same-reference-genome#latest I am trying to run CollectMultipleMetrics from Picard tools on a CRAM file but I get an "Sequences at index 0 don't match, but usin ...
gatk picard written 9 months ago by Niek De Klein2.5k
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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 10 months ago by Niek De Klein2.5k
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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 10 months ago by Niek De Klein2.5k
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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 10 months ago by Niek De Klein2.5k • updated 10 months ago by finswimmer11k
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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 22 months ago by Niek De Klein2.5k • updated 22 months ago by Pierre Lindenbaum121k
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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 23 months ago by Niek De Klein2.5k

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