User: Niek De Klein
Niek De Klein • 2.5k
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- Netherlands
- Last seen:
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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 8 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 9 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 9 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 9 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 9 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 10 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 10 months ago by
Niek De Klein • 2.5k
3
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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 10 months ago by
Niek De Klein • 2.5k
• updated
10 months ago by
finswimmer ♦ 11k
2
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735
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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 22 months ago by
Niek De Klein • 2.5k
• updated
22 months ago by
Pierre Lindenbaum ♦ 121k
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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 23 months ago by
Niek De Klein • 2.5k
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