2207 days ago
Installing pb-assembly on Linux !
...bcftools: 1.9-h4da6232_0 bioconda bedtools: 2.27.1-he9418...##########################################| Time: 0:00:00 3.76 MB/s bedtools-2.27. 100% |#################...2031 days ago
Setting up falconUnzip conda environments for genome assembly !
...ge avro-python2: 1.8.2-py_1 bioconda bcftools: 1.9-h4da6232_0 bioconda bedtools: 2.27.1-he9418...1987 days ago
Bash command to install GATK, Bedtools and SnpEff !
...g transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install bedtools Collecting package metadata...rkshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - bedtools The following packages w...1552 days ago
1439 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1363 days ago
Bash script to extract intronic fragments !
...he genic region, we have the intronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort | bedtools subtract -a stdin -b my_exon....1363 days ago
Bash script to get intergenic region from genome files !
...p/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort -g xxx.chrom.sizes | bedtools complement -i stdin -g xxx.ch...1363 days ago
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993 days ago