Results for "BAM"
Blogs
BBTools for bioinformatician !
...int the headers once. I have not tried that for bam output, only sam outputNote a..."quality count histogram". Filter SAM/BAM file by read length ...erage of the genome Program will take sam or bam, sorted or unsorted. Code:...2270 days ago
- ...functionality continues to be under development) # # --genome_guided_bam :genome guided mode, provide path to coordinate-sorted bam file. #...
2132 days ago
- +1 more Blogs
Bookmarks
Public Databases for Bioinformatics !
...p;https://www.encodeproject.org/files/ENCFF546PJU/@@download/ENCFF546PJU.bam, https://www.encodeproject.org/files/ENCFF059BEU/@@download/ENCFF059BEU.bam. Blacklisted regions were obt...1138 days ago
- ...f three statistically-based variant detection tools:* SAMtools: Mpileup* GATK: Unified Genotyper* FreeBayesEach of these tools takes as its input a BAM file of aligned reads and gen...
3652 days ago
- +45 more Bookmarks
Files
- ...local/bin/samtools sort -@ 20 -no - temporarySam > FALCON-Unzip-Scaff.bamMapping long-reads using blasr...'anchor_contig_info.dat': No such file or directorymv FALCON-Unzip-Scaff.bam FALCON-Unzip-Scaff-with-repea...
2150 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
...s by relieving investigators from the burdens of data preparation. SAMMate 2.7.4 / assemblySAM 1.1 – Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and...2685 days ago
Top-level pages
Structure of Binary files used for storing sequencing data-bam and sff
Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is tha...aximum information content. Link for those who looking for structure of Bam and sff file: Bam: http://s...3919 days ago
Next generation sequencing in R or bioconductor environment
...amtools provides functions for parsing and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly becoming a univers...ides support for importing into R short read alignment data in BAM format (via Rsamtools) and as...3624 days ago
- +6 more Top-level pages
Wire posts
News
ArrayGen Next Generation Genome Browser Coming Soon !!!
...is platform independent and much simpler to use. The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can be integrated with...3075 days ago
Release Notes for Genome Workbench 2.10.5
New Features in latest release New ProSplign tool integrated with Genome Workbench (Tutorial, Video) New export function for BAM/cSRA coverage graphs (Tutorial) New export...2914 days ago
Opportunity posts
One-Year Internship In Computational Biology & Bioinformatics
...ship requires a first class degree in Engineering Sciences (Biotechnology/Computer Science), Medical/Dental/Pharmaceutical Sciences (MBBS or BDS or BAM or B.Pharm) or a Masters degr...2952 days ago
Bio-Scripts
- zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc
2209 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get le...
2209 days ago
- +24 more Bio-Scripts
Tags
Structure of Binary files used for storing sequencing data-bam and sff
Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content. Link for those who looking for structure of Bam and sff file: Bam: http://samtools.sourceforge.net/SAMv1.pdf (from...Tags: bam, sff, sam, iontorrent data, 454 data, pyrosequencing data, hxd, hexadecimal, binary files, sequencing
3919 days ago
- To do sam to bam conversion, follow the following commands :- Code: $ samtools view -b -S file.sam > file.bam Then you will need to use Code: $ samtools sort file.bam file-sorted followed by Code: $ samtools index file-sorted.bam in order to get an indexed fil...
Tags: sam, bam, conversion
2290 days ago
Comments
Comment on "REAPR: a universal tool for genome assembly evaluation"
...nute. The next tool we need is reapr smaltmap which creates a bam file of read-pair mappings. D...ctmap and create an output file called <assembler>_smalt.bam. This should take about twent...1336 days ago
- ...nbsp; Set display to reads per million for BAM and TDF files. &nb...p; setGenome fasta|bam|genome ...
1519 days ago
- +4 more Comments
