User: rotemkat
rotemkat • 0
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Posts by rotemkat
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... Hi,
Is there a way to get the allele frequency of each mutation in dbSNP?
The data I downloaded from here ( ftp://ftp.ncbi.nih.gov/snp/organisms ) does not include it, but maybe there's another source I'm not familiar with? ...
written 18 days ago by
rotemkat • 0
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... Hi,
Is there a way to select which of the optional outputs to be actually produced and saved?
Currently I get 4 files (0000, 0001, 0002, 0003) and I actually need only one of them (the first).
Thanks ...
written 3 months ago by
rotemkat • 0
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... Hi,
I need to create a tab-delimited file using via matlab.
I have a cell array and two line of headers I need to add before the actual data:
1: `##fileformat=VCFv4.0`
2: `#CHROM POS ID REF ALT QUAL FILTER INFO `
so for the second line I created:
header={'#CHROM','POS','ID','REF','ALT','QU ...
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Comment:
C: Loop using BCFTOOLS ?
... I think part of my problem is because the list of mutations is not in a vcf file, but just txt file.
I tried to save it as vcf and tried the following commands:
```./bcftools isec -p myList.vcf.gz dbSNP.vcf.gz```
---> Expected multiple files or the --targets option
``` ./bcftools isec -C /myLis ...
written 3 months ago by
rotemkat • 0
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Comment:
A: Loop using BCFTOOLS ?
... Hi, Thanks!
Still having problem, can you elaborate a bit?
Also, can I use the second list as csv/xlsx file? or i have to find a way to convert it to vcf file?
Thanks!!! ...
written 3 months ago by
rotemkat • 0
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... Hi!
I have a list of mutations, and I want to know which of them are germline mutations and appear in the dbSNP (I downloaded the VCF file).
Is there an efficient way to run over this list using bcftools, rather than going line by line and filter the dbSNP accordingly?
Thanks!! ...
written 3 months ago by
rotemkat • 0
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... I still get multiple errors =/
$ ./bcftools filter -i 'CHROM==1' /path/file.vcf | bcftools stats | grep TSTV
-bash: bcftools: command not found
[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
Error: cannot use arithmetic operat ...
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... I tried to follow the instructions here: https://samtools.github.io/bcftools/
being in the following path - /Users/my_username - i followed the commands and indeed now i have the bcftools folder.
Then, I want to filter my VCF file, so I did the following: (based on the instructions here: https://sa ...
written 4 months ago by
rotemkat • 0
• updated
4 months ago by
finswimmer ♦ 13k
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... Hi!
I have a list of mutations and I want to check how many of them are germline mutations and appear in the dbSNP.
I download the VCF file from dbSNP, but this is a very heavy file and i can't find a way to upload it and compare it with my list.
Do you have any ideas for a solution for what i need? ...
written 4 months ago by
rotemkat • 0
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... Hi,
I have a dataset (from GEO) that includes the expression values of multiple tumor cells and normal cells. I would like to know the expression of CAF cells and have the signature of the relevant genes... How can i do it? or is there a simpler way to find the expression of CAF cells?
Thanks ...
written 11 months ago by
rotemkat • 0
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For enrichment of transcription factors
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