Download a bam alignment file
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 Supplying a reference file will enable base alignment quality calculation for all reads aligned to a reference in the file.
Tools for early stage alignment file processing. Contribute to gt1/biobambam2 development by creating an account on GitHub.
-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. Learning the Sequence Alignment/Map format. Contribute to davetang/learning_bam_file 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
Population-scale detection of novel sequence insertions - bkehr/popins
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 Supplying a reference file will enable base alignment quality calculation for all reads aligned to a reference in the file. 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
ngsLCA/ngsLCA -editdistmin 0 -editdistmax 5 -names ncbi_tax_dmp/names.dmp.gz -nodes ncbi_tax_dmp/nodes.dmp.gz -acc2tax ncbi_tax_dmp/nucl_gb.accession2taxid_24april.gz -bam sorted_bam_file.bam -outnames outfile.ed0
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 Supplying a reference file will enable base alignment quality calculation for all reads aligned to a reference in the file. 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.
Basic ChIPseq pipeline, from downloading Fastq files to calling ChIP peaks. Coded in bash and Perl - alfonsosaera/ChIPseq
Under the User menu, select Register to create a new account. Next, complete the registration form. 3 BAM files are typically compressed and more efficient for software to work with than SAM. SAMtools makes it possible to work directly with a compressed BAM file, without having to uncompress the whole file. 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.