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Questions - genome

define SAMPLE for different dir name and sample name in snakemake code

I have written a snakemake code to run bwa_map. Fastq files are with different folder name and different sample name (paired end). It shows error as 'SAMPLES' is not defined. Please help. Error: $snak...
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Himanshu Singh

pipeline

bioinformatics

snakemake

genome

Votes: 0

Answers: 1

Latest Answer

The specific error you are seeing is because the variable SAMPLES isn't set to anything before you use it in expand. Some other issues you may run into: Output file is missing the {sample} wildcard. ...
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Troy Comi

select uniquely mapped genes to SNP

I have a vcf and want to select 100 genes, and for each gene, to select one SNP? Technically if we consider one gene it has many rsid mapped to it. For my analysis I need to select 100 genes and for e...
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Rhea Bedi

r

filter

code-generation

genome

vcf-variant-call-format

Votes: 0

Answers: 1

Latest Answer

Consider str.split of the pipe-delimited column in ANN for the gene which is about the fourth pipe. Then run a sequential count by the gene grouping with ave. Then subset group number for the 1. Pleas...
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Parfait

How to write a batch script for IGV that directly leads me to my chosen BP range on each chromosome

as input for the script I have a list of BP ranges on several chromosomes and I am wondering how to write an IGV script that directly leads me only to these areas, without showing the whole chromosome...
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Human

bioinformatics

viewer

genome

Votes: 0

Answers: 0

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