Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655....nment with bwa: bwa mem -t $threads -R '@RG\tID:K12\tSM:K12' ---...s says "align using so many threads" and also "give the reads th...: samtools view -b - --- this reads SAM from stdin (the - specif...l it we're working with short read data...1612 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] password for jit: R version 3.4....ong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o gc...1602 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencin...d -$N > selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data f...merge -f all.bam bam/*.bam # Investigate the readgroups...1595 days ago
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Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1336 days ago
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Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name...1099 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r my...1097 days ago
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt1049 days ago