Contents
What is an rg tag in BAM file?
RG: Read group, which indicates the number of reads for a specific sample. ▶ BC: Barcode tag, which indicates the demultiplexed sample ID associated with the read.
What does a BAM file contain?
A BAM file (. bam) is the binary version of a SAM file. A SAM file (. sam) is a tab-delimited text file that contains sequence alignment data.
What is NH tag?
The other way to tell multiple hits is to use the optional tag NH (if any). NH is “Number of reported alignments that contains the query in the current record”, which should be >1 for multiple-mapped reads.
How do you convert SAM to Bam?
To convert SAM to BAM, we use the samtools view command. We must specify that our input is in SAM format (by default it expects BAM) using the -S option. We must also say that we want the output to be BAM (by default it produces BAM) with the -b option.
What is a BAM and SAM file?
The SAM format consists of a header and an alignment section. The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. SAM files can be analysed and edited with the software SAMtools.
How many license plates does NH require?
two license plates
Does New Hampshire require two license plates to be displayed? Yes.
Do you need a title to register a car in NH?
New Hampshire is a title required state, and title to a motor vehicle must be proven before registration can be obtained. Please note that the only acceptable proof of ownership is the actual title. Photocopies or faxed copies are unacceptable.
What is unaligned Bam?
Half-sequence and half mythical-beast, “unaligned” BAM files are used to store FASTQ files. SAM/BAM are alignment formats, thus it feels quite anachronistic to use them to store “unaligned” sequences. There are many tools that can operate on BAM files (extract by tags, filter by tags, etc)
What do you write to a merged BAM file?
Merged SAM or BAM file to write to. Reference sequence file. Original SAM or BAM file of unmapped reads, which must be in queryname order. Reads MUST be unmapped. Adds the mate CIGAR tag (MC) if true, does not if false.
How to add a graph to a BAM file?
The steps for this part are identical to Steps 1 and 2 in this tutorial, however with a different data file. From the File menu choose Open and select BAM files from the left side. Select button on the right that says Add a BAM file. Navigate to the BAM Test Files folder you downloaded select with_index_with_graph.
Where do I find the index file for BAM?
For viewing BAM files, an index file must be found in the same directory as the BAM file. The index should be named by appending “ .bai ” to the BAM file name. If there is no index file, you can use SAMTools to create one (please download SAMTools from http://samtools.sourceforge.net and install locally).
How do I export an alignment table in Bam?
From the Graphical Sequence Viewer, zoom to the desired location and select a range of interest. Right-click the selected range and click the Export Data option in the context menu. An alignment export menu will be opened. Note that BAM files are stored as alignments, so you need to select “ Alignment Table File ” in the list on the left.