SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: Specifications of SAM/BAM and related high-throughput sequencing file formats - samtools/hts-specs microRNA profiling pipeline. Contribute to bcgsc/mirna development by creating an account on GitHub. Porting of samtools-ruby to BioRuby. Binder of samtools for ruby, on the top of FFI -from original project- - helios/bioruby-samtools Dockerfile for Alignment. Contribute to statgen/docker-alignment development by creating an account on GitHub. k-mer based base quality recalibration. Contribute to adamjorr/kbbq development by creating an account on GitHub.
RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format). - vimalkvn/riboplot
Melt Manual - Free download as PDF File (.pdf), Text File (.txt) or read online for free. Melt Manual At this point it is highly recommended that if you want to use a previously aligned BAM file for allelotyping, that you first run lobSTR alignment on the BAM file and then proceed with the regular instructions. The information about the references is encoded in the header, in the @SQ lines. bam-mergeRef adds an alternative name flag (AN) with the name of the chromosome (or sequence), the reference ID provided to bam-mergeRef and the file number… a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool - betteridiot/bamnostic -o * output directory -r * reference genome -v * VCF file or directory --gz flag denoting VCF files are gzipped --rnaedit ** flag to N-mask rna editing sites -e ** file containing RNA editing sites, can be downloaded from Radar (http… Contribute to nygenome/nygc-short-alignment-marking development by creating an account on GitHub.
Basic ChIPseq pipeline, from downloading Fastq files to calling ChIP peaks. Coded in bash and Perl - alfonsosaera/ChIPseq
The information about the references is encoded in the header, in the @SQ lines. bam-mergeRef adds an alternative name flag (AN) with the name of the chromosome (or sequence), the reference ID provided to bam-mergeRef and the file number… a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool - betteridiot/bamnostic -o * output directory -r * reference genome -v * VCF file or directory --gz flag denoting VCF files are gzipped --rnaedit ** flag to N-mask rna editing sites -e ** file containing RNA editing sites, can be downloaded from Radar (http… Contribute to nygenome/nygc-short-alignment-marking development by creating an account on GitHub.
Upload a BAM file or select an uploaded BAM file to convert it to BED or bigBed format. The conversion takes care of spliced aligments: Alignments containing skipped regions ('N' in the Cigar string) result in several data records in the BED…
Workshop material. Contribute to lletourn/Workshops development by creating an account on GitHub. Validation and manipulation of Fastq files, scRNA-seq barcode pre-processing and UMI quantification. - nunofonseca/fastq_utils A Pilot 1 bam file (plus .bas file): NA18940.SLX.maq.SRP000031.2009_09.unmapped.bam has been added to the ftp site. The new version contains corrected library information. Calculate statistics for Oxford Nanopore sequencing data and alignments
CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file formats. The files include: per chromosome files with genotypes for all samples, a genome wide sites file and genotype files for each of the supporting call sets. Remove primer sequence from BAM alignments by soft-clipping - tommyau/bamclipper Get repeat alignment statistic from BAM/SAM file. Contribute to lidaof/iteres development by creating an account on GitHub. Contribute to swyder/Genomic_Utilities development by creating an account on GitHub.
Researchers who wish to use the mapping tools with known indel positions as well as with SNPs—for instance if they have sequenced their crossing strain—may do so with no modifications to the tool.] Prior to running the plotting tool, we…
Workshop material. Contribute to lletourn/Workshops development by creating an account on GitHub. Validation and manipulation of Fastq files, scRNA-seq barcode pre-processing and UMI quantification. - nunofonseca/fastq_utils A Pilot 1 bam file (plus .bas file): NA18940.SLX.maq.SRP000031.2009_09.unmapped.bam has been added to the ftp site. The new version contains corrected library information.