User: 2012secondseason

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Posts by 2012secondseason

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Comment: C: Difference between 'intergenic' and 'ncRNA' in annotation.
... Thank you for answer. But still confused. 'intergenic region means intron? And of course it doesn't code protein?? What's functional difference with intron?? ...
written 10 months ago by 2012secondseason10
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Difference between 'intergenic' and 'ncRNA' in annotation.
... Hi all. I am confused about the concept of 'Intergenic' region in annotation. What's difference between ncRNA? ncRNA means only 'long' non-coding rna? Thanks in advance. ...
annotation ncrna intergenic annovar written 10 months ago by 2012secondseason10 • updated 10 months ago by WouterDeCoster37k
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When Hard clipping is used instead of the Soft clipping ?
... Hi all. The documentation for Samtools is minimal at best. I'm still confused on the concept of a clipped read. I know that there are many explanations here that soft clipped bases are present in SEQ unlike hard clipped bases. But it's insufficient. In what cases, use H instead of S ?? Thanks. ...
clipping cigar hard clipping written 11 months ago by 2012secondseason10 • updated 11 months ago by Devon Ryan88k
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(Closed) In SAM format, what is SN:GL000212.1 ?
... Hello. Studying SAM format , I am anxious about 'GL' in Recerence suquence name field like this. @SQ SN:GL000207.1 LN:4262 @SQ SN:GL000226.1 LN:15008 @SQ SN:GL000229.1 LN:19913 @SQ SN:GL000231.1 LN:27386 @SQ SN:GL000210.1 LN:27682 @SQ SN:GL000239.1 LN:33824 @SQ ...
reference samformat written 11 months ago by 2012secondseason10
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(Closed) What is the relation between contig and reference sequence in VCF format?
... As far as I know, Contig is a combination of continuous & overlapping reads. But in description of VCF format, there is a URL of reference in Contig field like this. 1.2.7 Contig field format As with chromosomal sequences it is highly recommended (but not required) that the header include tags ...
contig reference written 11 months ago by 2012secondseason10
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Comment: C: What is URL of Contig in VCF format?
... Thanks. But why is reference sequence's url there?? What is the relation between contig and reference sequence? ...
written 11 months ago by 2012secondseason10
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What is URL of Contig in VCF format?
... Hi.. I am very confused with contig's url. I know that contig means combination of sample's continuing & overlapping regional reads, but why 'URL' is in Contig's field? That url means what? 1.2.7 Contig field format As with chromosomal sequences it is highly recommended (but not required ...
contig written 11 months ago by 2012secondseason10 • updated 11 months ago by RamRS20k
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(Closed) How To Interpret contig field Fields In Vcf Files From 1000 Genomes?
... Hello. There are 3 contigs about chromosome 1 in a 1000 genome indels vcf file.(1000G_phase1.indels.hg19.vcf) ##contig= ##contig= ##contig= I dont understand what 'assembly' exactly means. In fact, I don't fully understand how breakpoint are assembled. contig, breakpoint, indel, assembly. How th ...
vcf contig breakpoint written 11 months ago by 2012secondseason10 • updated 11 months ago by Pierre Lindenbaum118k
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How do we get VCF's ALT field values?
... Hi. When I use bcftools only with input BCF file, VCF file involving ALT filed values is created. I am wondering bcftools has autonomously informations for altarnatice alleles. Thanks. ...
vcf alt bcftools written 11 months ago by 2012secondseason10
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Comment: C: What's 1000 Genome indel calls??
... Nice explanation. Thank you very much! ...
written 11 months ago by 2012secondseason10

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