Results for "sam"
Bio-Scripts
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.bai2173 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
- ....0 ➜ nextsv git:(master) pip install pysam Requirement already satisfied: pysam in /home/urbe/anaconda3/lib/p...0/src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o [ 22%] Building.../CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o [ 53...
2089 days ago
- ...age-4.0.2.1-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async...(BETA Tool) Counts reads in the input SAM/BAM GetPileupSummaries...Tools that manipulate read data in SAM, BAM or CRAM format AddC...
2065 days ago
- ...0k-sv2.2/orig/sv2.fasta.gz 1 18.6M 1 256k 0 0 94979 0 0:03:26 0:00:02 0:03:24 94945greg200k-sv2.2/README.txt greg200k-sv2.2/SAM.txt greg200k-sv2.2/makefile...
2024 days ago
- ...am_io.h htslib-1.9/cram/cram_samtools.c htslib-1.9/cram/cram_...ANS_static.h htslib-1.9/cram/sam_header.c htslib-1.9/cram/sam...ndian.c htslib-1.9/test/md#1.sam htslib-1.9/test/md.fa htsli...ex.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram...
2009 days ago
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...2009 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1716 days ago
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
