BOL: Results for "SAM"

Results for "SAM"

- Jit@jit.aber
Jit
Skills: SAM tool
580 days ago
- Mansi Gill@mansigill1987
Mansi Gill
About me: kartikeya sharma information tv kartikeya sharma itv Kartikeya Sharma
3098 days ago

- Jit@jit.aber
Computer simulation of genetic mechanism !!
...tions from allele data frequencies http://www.ensam.inra.fr/urlb/bottleneck/bottl..., employing a minimal set of parameters. http://sammeth.net/confluence/display/si...modifying Hudson's ms software to generate samples of DNA sequences with a b...
2965 days ago
- Archana Malhotra@archana
Software and Tools to detect structure variation with long reads !!
...utput from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled! Mo...ture" regions Genotyping of SVs with Illumina paired-end reads from WGS samples More at https://g...
2598 days ago
+1 more Blogs

- Jitendra Narayan@admin
CrossMap
...as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/...
2999 days ago
- Neelam Jha@neelam
Picard
...r manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF spe...
2918 days ago
+26 more Bookmarks

- Jit@jit.aber
Genome Assembly Tools and Software - PART2 !!
...set of aligned sequence reads in a SAM file and a set of variant cal...om ultra-deep sequencing of a mixed sample. The package contains prog...m the burdens of data preparation. SAMMate 2.7.4 / assemblySAM 1.1 &...ds by using either a model-based or sampling-based simulation. SIS &...
2676 days ago

- Jitendra Narayan@admin
Bioinformatics Algorithms
...reduces an instance of a problem to one or more smaller instances of the same problem (usually recursively...lecture/nlp18new/index.htm•http://www.cse.ucsc.edu/research/compbio/sam.html SAM Software for HM...
3936 days ago
- Jitendra Narayan@admin
Bioinformatics Courses Around the World
...Computational Biology (Newark, New Jersey) Sequence Alignment and Modeling System (Documentation for SAM) Technical University of Den...
3934 days ago
+16 more Top-level pages

- Jit@jit.aber
Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam #Extract #Ids #SAM #BAM #NGS
3625 days ago
- Jit@jit.aber
Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}' #SAM #BAM #Samtools #Tricks #NGS
2856 days ago
+12 more Wire posts

- Nidhi Rajput@nidhi
Bioinformatics WalkIn at NII
...should have knowledge of the following: Programming: Perl and Python. Operating system: Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy...
3156 days ago

- Jit@jit.aber
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
- Jit@jit.aber
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.bai
2173 days ago
+14 more Bio-Scripts

- Jit@jit.aber
Comment on "URMAP, an ultra-fast read mapper"
...ome index filename is given by the -ufi option. A filename for SAM format output is specified by -samout. Use /dev/stdout or "-" (m...reate the file. Example urmap -map reads.fastq -ufi hg38.ufi -samout reads.sam
1274 days ago
- BioStar@biostar
Comment on "Sibelia: A comparative genomics tool"
...variable or input files are in the same folder with "Sibelia" execut...index numbers of sequences (in the same order as they apper in the i...a synteny block. Copies having the same number in the "tag" field (l...gluing "stripes" consisting of the same synteny blocks. For example,...
1275 days ago
+11 more Comments