User: banerjeeshayantan
banerjeeshayantan • 50
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Posts by banerjeeshayantan
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C: COSMIC to Ensembl mapping
... Thanks for the suggestion. Will surely check it out ...
written 23 days ago by
banerjeeshayantan • 50
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C: COSMIC to Ensembl mapping
... Thanks for your reply. So my question is do I need to incorporate variant information in the reference sequence? What if the flanking region for a SNP is part of a INDEL. If I don't incorporate the INDEL variant into the refseq, wouldn't I lose information? Or should I just use the refseq as it is? ...
written 23 days ago by
banerjeeshayantan • 50
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... The vcfs were downloaded from COSMICdb ...
written 23 days ago by
banerjeeshayantan • 50
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Comment:
C: COSMIC to Ensembl mapping
... The flanking region containing the variant ...
written 23 days ago by
banerjeeshayantan • 50
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Comment:
C: COSMIC to Ensembl mapping
... Sorry for the confusion. I meant flanking sequence containing the variant position ...
written 23 days ago by
banerjeeshayantan • 50
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... I have downloaded the COSMIC mutation file based on GRCH38. I have the cosmic mutation ids for each mutation (eg, COSM521,COSM520 etc). If I copy these ids and check in the search box of the website I get all the related information such as its emsembl contig etc. Using these ENSEMBL contigs, I visi ...
written 24 days ago by
banerjeeshayantan • 50
• updated
23 days ago by
Emily_Ensembl ♦ 15k
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... I am trying to find bcftools consensus using GRCH38. But I am getting the following error. What does this mean and how to get past it? The command used was: **consensus -f grch38.fa CosmicCodingMuts.vcf.gz > real_nbd.fa**
Warning: Sequence "CM000672.2" not in CosmicCodingMuts.vcf.gz
War ...
written 24 days ago by
banerjeeshayantan • 50
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... I am using *bedtools getfasta* to extract some sequences from the reference genome, hg38. I have the bed file ready but the chromosome numbering is like `1,2,3,...,25`.
In my `hg38.fa`, however the chromosomes are numbered from `1,2,3, ...,X,Y,Mt`. This is the reason I am not able to get fasta sequ ...
written 28 days ago by
banerjeeshayantan • 50
• updated
27 days ago by
zx8754 ♦ 4.5k
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... I am trying to incorporate variants in my ref.fa file using bcftools consensus. But the output consensus.fa has only one chromosome (the first one from the ref.fa file). Why are the other chromosomes not showing up in consensus .fa?
The command used was :
bcftools consensus -f hg38.fa compresse ...
written 28 days ago by
banerjeeshayantan • 50
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... I have generated a consensus sequence of a bam file using
samtools mpileup -uf /media/shayantanbanerjee/disk21/Ref/hg38.fa stjude.bam | bcftools call -c | vcfutils.pl vcf2fq > cns_stjude.fq
Now I want to find how close this file is to the human reference hg38.fa. How can I do that? I a ...
written 4 weeks ago by
banerjeeshayantan • 50
• updated
4 weeks ago by
genomax ♦ 50k
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