User: Niek De Klein
Niek De Klein • 2.5k
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Posts by Niek De Klein
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... 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 12 months ago by
Niek De Klein • 2.5k
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... 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 13 months ago by
Niek De Klein • 2.5k
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... 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 13 months ago by
Niek De Klein • 2.5k
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... 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 13 months ago by
Niek De Klein • 2.5k
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... 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 ...
written 13 months ago by
Niek De Klein • 2.5k
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... 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 months ago by
Niek De Klein • 2.5k
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... Thanks, I'm testing this now and seeing how it compares to removing secondary aligned reads ...
written 15 months ago by
Niek De Klein • 2.5k
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6 follow
1
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... 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 ...
written 15 months ago by
Niek De Klein • 2.5k
• updated
15 months ago by
finswimmer ♦ 13k
2
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1
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859
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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 2.3 years ago by
Niek De Klein • 2.5k
• updated
2.3 years ago by
Pierre Lindenbaum ♦ 124k
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... 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 2.3 years ago by
Niek De Klein • 2.5k
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