User: chevivien

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chevivien60
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China
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4 years, 3 months ago
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Posts by chevivien

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Should unplaced scaffolds in reference genome be used to map newly sequenced gen
... Thanks for the input. ...
written 4 months ago by chevivien60
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Comment: C: [E::hts_idx_push] chromosome blocks not continuous :Indexing of gff3 files using
... Thanks, this option sort -k1,1 doesn't work , sortlines in genome tools worked. ...
written 4 months ago by chevivien60
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[E::hts_idx_push] chromosome blocks not continuous :Indexing of gff3 files using tabix error
... Has anyone encountered this error before and could help? I am trying to index gff files using tabix in samtools and gt gff (genome tools) but getting errors. I did this grep -v "#" sample.gff | sort -k1,1n -k4,4n -k5,5n | bgzip -c > sample2.gff3.gz tabix -p gff sample2.gff3.gz I g ...
gff3 tabix samtools gt gff genometools written 4 months ago by chevivien60 • updated 4 months ago by WouterDeCoster23k
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Comment: C: CNVnator error :Can't determine length for 'chr1'. No reference genome specified
... It's running well now. Thanks ...
written 5 months ago by chevivien60
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Qualimap abnormally high coverage standaed deviation
... Hii , I have run BAM files QC using qualimap and I am getting below output for the coverage mean standard deviation 36.5977 849.6354 I find the standard deviation to be abnormally high. Is this normal? ...
bamqc coverage standard deviation written 5 months ago by chevivien60
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Should unplaced scaffolds in reference genome be used to map newly sequenced genome
... Hii, Is it in order to map unplaced scaffolds in reference genome against newly sequenced genome when carrying out reference based assembly? Or it is just ok to use placed chromosomes e.g (ch1-chr29 basing on the number of chromosomes in ref genome) . The purpose of the analysis is to obta ...
unplaced scaffolds reference based assembly cnv written 5 months ago by chevivien60 • updated 4 months ago by Vijay Lakhujani1.3k
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Comment: C: CNVnator error :Can't determine length for 'chr1'. No reference genome specified
... The genome file ((sample.fa) is here /home/vchebii/cnv/sample.fa and the chrom files are here as well /home/vchebii/cnv/ Actually, I am running the cnvnator in the directory where all input files are. ...
written 5 months ago by chevivien60
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Comment: C: CNVnator error :Can't determine length for 'chr1'. No reference genome specified
... Bam files are named like this @SQ SN:chr1 LN:157403528 @SQ SN:chr2 LN:136510947 @SQ SN:chr3 LN:120038259 Chrom fasta files are named like this chr1.fa, chr2.fa, chr3,fa e.t.c. Chrom fasta headers and reference genome looks like this: >chr1 ...
written 5 months ago by chevivien60
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CNVnator error :Can't determine length for 'chr1'. No reference genome specified.
... Hii, I am getting this error when creating histograms using cnvnator Allocating memory ... Can't determine length for 'chr1'. No reference genome specified. Done. Calculating histograms with bin size of 100 for 'chr1' ... This is the command I am using Command option 1: cnvnator -genome /hom ...
no reference genome cnvanator cnv written 5 months ago by chevivien60 • updated 5 months ago by rbagnall1.1k
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Comment: C: From bam paired files to fasta
... Hii Albert, Thank you for the suggestion. So basically with whole genome data assembled by reference mapping , pulling out protein coding genes or mRNA is complicated assignment? My main goal is to get extract protein coding genes from this data for downstream work before embarking on denovo asp ...
written 6 months ago by chevivien60

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