User: banerjeeshayantan

Reputation:
50
Status:
Trusted
Location:
Last seen:
3 days, 22 hours ago
Joined:
2 years, 11 months ago
Email:
b****************@gmail.com

Posts by banerjeeshayantan

<prev • 132 results • page 1 of 14 • next >
0
votes
1
answer
168
views
1
answers
Comment: C: COSMIC to Ensembl mapping
... Thanks for the suggestion. Will surely check it out ...
written 23 days ago by banerjeeshayantan50
0
votes
1
answer
168
views
1
answers
Comment: 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 banerjeeshayantan50
0
votes
0
answers
89
views
0
answers
Comment: C: Warning while finding bcftools consensus
... The vcfs were downloaded from COSMICdb ...
written 23 days ago by banerjeeshayantan50
0
votes
1
answer
168
views
1
answers
Comment: C: COSMIC to Ensembl mapping
... The flanking region containing the variant ...
written 23 days ago by banerjeeshayantan50
0
votes
1
answer
168
views
1
answers
Comment: C: COSMIC to Ensembl mapping
... Sorry for the confusion. I meant flanking sequence containing the variant position ...
written 23 days ago by banerjeeshayantan50
1
vote
1
answer
168
views
1
answer
COSMIC to Ensembl mapping
... 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 ...
assembly next-gen cosmic ensembl written 24 days ago by banerjeeshayantan50 • updated 23 days ago by Emily_Ensembl15k
0
votes
0
answers
89
views
0
answers
Warning while finding bcftools consensus
... 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 ...
assembly next-gen sequencing written 24 days ago by banerjeeshayantan50
3
votes
1
answer
145
views
1
answer
Difference in chromosome numbering
... 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 ...
bedtools R next-gen fasta written 28 days ago by banerjeeshayantan50 • updated 27 days ago by zx87544.5k
0
votes
0
answers
93
views
0
answers
BCFtools consensus sequence
... 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 ...
next-gen written 28 days ago by banerjeeshayantan50
0
votes
0
answers
74
views
0
answers
Similarity between reference files
... 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 ...
assembly sequencing written 4 weeks ago by banerjeeshayantan50 • updated 4 weeks ago by genomax50k

Latest awards to banerjeeshayantan

Centurion 8 weeks ago, created 100 posts.
Supporter 10 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1957 users visited in the last hour