User: 4galaxy77

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4galaxy7730
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New User
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United Kingdom
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1 month, 3 weeks ago
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3 years, 7 months ago
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Posts by 4galaxy77

<prev • 26 results • page 1 of 3 • next >
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automatically create index files from output in bcftools
... say i am running a command in bcftools like /share/apps/genomics/bcftools-1.9/bin/bcftools view -O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz -R $variants --exclude-types indels $sample Rather than then having to run a separate command on the output file to produce an index file: ...
software error written 3 months ago by 4galaxy7730 • updated 3 months ago by Kevin Blighe42k
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Comment: C: filtering by POS in bcftools
... Yeah, I figured. Actually found the answer here, so you can close the thread https://www.biostars.org/p/170965/ thanks. ...
written 3 months ago by 4galaxy7730
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Comment: C: filtering by POS in bcftools
... sorry im not sure the difference. I tried reading the manual, but I didn't follow.. I have a txt file of positions: 1324324 4325435 etc and within the vcf file, SNPs with those positions. I would like to create a new vcf file, which is a subset of the first, only containing those SNP ...
written 3 months ago by 4galaxy7730
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filtering by POS in bcftools
... Hi, I have a vcf file which I would like to filter by a list of SNP positions, which are present in a positions.txt file. bcftools filter -i 'POS=@positions.txt' input.vcf.bgz > output.vcf However, this says: Error: could not parse the expression. Note that the "@file_name" syntax ca ...
software error bcftools written 3 months ago by 4galaxy7730 • updated 3 months ago by finswimmer11k
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Comment: C: How to get "best guess" genotypes after running Beagle 4.1
... The most likely genotype configuration is the two numbers separated by the pipe "|" symbol, for example, the most likely configuration at the first individual is 0|1, a homozygote, and 0|0, a homozygote at the second individual. ...
written 6 months ago by 4galaxy7730
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Filtering blastx by taxonomy ID
... If I am locally running a blastx against the nr database I downloaded, is it possible to specifiy only hits to mammals (taxid = 40674), for example? My blast run is taking quite a long time and I am hoping that it might speed it up if I filter for the taxonomy I am interested in. Or is this somethin ...
genome software error blast written 23 months ago by 4galaxy7730
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Comment: C: blast database formatting issue
... I was running the first blastn run on a cluster and then checked the database index locally, hence the different paths :) I didn't realise I was running an old version - the source file says ncbi-blast-2.6.0+ - so I'll update it and try again. Thanks. ...
written 2.0 years ago by 4galaxy7730
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blast database formatting issue
... Hi, I downloaded the nt nucleotide database using: $ ./update_blast.pl nt --decompress Which seemed to work fine - all the files from nt.00 to nt.46 are present. I went to use the database and the same error came up $ blastn -db /home/ucbtsm6/Scratch/database/nt -num_threads 8 -evalue ...
software error blast written 2.0 years ago by 4galaxy7730 • updated 2.0 years ago by Michael Dondrup46k
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Comment: C: Testing for significant clustering in dendrograms of gene expression
... thank you for your help. i will have a look at this. ...
written 2.1 years ago by 4galaxy7730
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Comment: C: Testing for significant clustering in dendrograms of gene expression
... Ah that looks perfect, thanks! ...
written 2.1 years ago by 4galaxy7730

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