Palindrome Simulation commands !
...Simulated.fa 3319 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa...o paired_dat 3320 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa...1726 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2174 days ago
Long reads mapper bash script !
...tion ready !" #Location of the tools samtools=/home/urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/...sta $longReads -t $thread > $fileName.out.sam elif [ $toolName == "lamsa"...sta $longReads -t $thread > $fileName.out.sam elif [ $readsType == "pacbi...2113 days ago
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Installing Platypus on Ubuntu !
...regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -...ocal/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/...O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/p...2010 days ago
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Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### converti...: use reference genome given samtools mpileup -g -f sal_ref_se...ne liner to count mean depth samtools depth -a sorted_dupremov...1593 days ago