User: chevivien

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chevivien70
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70
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Location:
China
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3 months, 1 week ago
Joined:
4 years, 9 months ago
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Posts by chevivien

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Is Pindel slow for everyone, or should I review my command?
... I am having the same problem with Pindel. How did you sort it out? ...
written 4 months ago by chevivien70
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Comment: C: Should unplaced scaffolds in reference genome be used to map newly sequenced gen
... Thanks for the input. ...
written 10 months ago by chevivien70
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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 10 months ago by chevivien70
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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 10 months ago by chevivien70 • updated 10 months ago by WouterDeCoster28k
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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 11 months ago by chevivien70
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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 11 months ago by chevivien70
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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 11 months ago by chevivien70 • updated 10 months ago by Vijay Lakhujani2.1k
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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 11 months ago by chevivien70
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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 11 months ago by chevivien70
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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 11 months ago by chevivien70 • updated 11 months ago by rbagnall1.2k

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