User: al.bodrug

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al.bodrug50
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Posts by al.bodrug

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Does it make any sense to make a kmer analysis in assembled sequences?
... Hello everyone, Most of us working on large repetitive genomes are probably familiar with the kmer distribution analysis on raw short reads, where we find the peak for the diploid portion of the genome, a hunch in case of polyploidy and a smaller flatter peak for the duplicated portion of the geno ...
genome assembly sequence written 8 months ago by al.bodrug50 • updated 8 months ago by Corentin450
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Comment: C: SAM FLAG for primary alignments, secondary alignments and what's their relations
... bowtie2 has XS and AS tags that report primary score (AS) and secondary score (XS). If they are similar it means that there are several (at least 2) similar alignments (similar/same aligning score in two different locations). You can use them to extract the uniquely aligning reads where unique means ...
written 10 months ago by al.bodrug50
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Answer: A: Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
... Note: PV4 seems to be supported /appear only when you call the variants with -c parameter in bcftools ...
written 10 months ago by al.bodrug50
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Answer: A: How to select uniquely and concordantly reads from hisat2 alingment for raw read
... I think like this you're gonna end up with unpaired reads where one of the mates has a ZS tag and the other doesn't and is the only one kept. So they won't be concordant. ...
written 10 months ago by al.bodrug50
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bowtie2 paired end read alignment yieldsscaffold information for unmapped reads
... The command I used: bowtie2 --fr -p 30 -x $GENOME -I 200 -X 800 -1 $READ1 -2 READ2 -S $SAM I wanted to extract unmapped reads. When using samtools view -f0x4 I obtain unmapped pairs and pairs where one of the mates is mapped and the other is not mapped. In the latter case, both mates have a sc ...
bowtie2 unmapped tlen read alignment written 22 months ago by al.bodrug50 • updated 21 months ago by Biostar ♦♦ 20
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Answer: A: Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
... Here it the latest version of samtools manual: http://www.htslib.org/doc/samtools.html PV4 field disappears. ...
written 22 months ago by al.bodrug50
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Variant calling: GT field disagrees with DP4 field
... I am calling variants from ~100 samples jointly with the consensus caller in bcftools. I request the DP4 field (deprecated) which reports the number of reads which support [reference_forward, reference_reverse, variant_forward, variant_reverse]. The genotype provided in the GT fields often disagrees ...
snp gt genotype dp4 written 2.4 years ago by al.bodrug50 • updated 2.4 years ago by Biostar ♦♦ 20
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Comment: C: Gene prediction and genome assembly
... Even if it does not inform you directly of the quality of the assembly, the number of genes found in the assembly indicates that what you have is a biologically possible molecule. That means that even if your assembly contigs are not exact, they are plausible. However if you don't find all or most e ...
written 5.7 years ago by al.bodrug50

Latest awards to al.bodrug

Scholar 22 months ago, created an answer that has been accepted. For A: Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?

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