Contents
What are supplementary reads?
Supplementary Alignment: A chimeric reads but not a representative reads. Primary Alignment and Secondary Alignment: A read may map ambiguously to multiple locations, e.g. due to repeats. Only one of the multiple read alignments is considered primary, and this decision may be arbitrary.
What is in SAM file?
SAM stands for Sequence Alignment/Map format. It is a TAB-delimited text format consisting of a header section, which is optional, and an alignment section. If present, the header must be prior to the alignments. Header lines start with ‘@’, while alignment lines do not.
Are BAM files smaller than SAM files?
BAM files take up much less space than SAM files. For archiving purposes, keep only the BAM file. The SAM file can easily be regenerated (if ever needed).
What is unmapped BAM?
uBAM is a variant form of the BAM file format in which the read data does not contain mapping information. Most sequencing providers generate FASTQ files with the raw unmapped read sequences, so that is the most common form in which the data is input into the mapping step of the pre-processing pipeline.
How does a BAM file look?
bam) is the compressed binary version of a SAM file that is used to represent aligned sequences up to 128 Mb. Header—Contains information about the entire file, such as sample name, sample length, and alignment method. Alignments in the alignments section are associated with specific information in the header section.
Which is easier to read, BAM or Sam?
Examples: To do anything meaningful with alignment data from BWA or other aligners (which produce text-based SAM output), we need to first convert the SAM to its binary counterpart, BAM format. The binary format is much easier for computer programs to work with. However, it is consequently very difficult for humans to read.
How to convert Bam to Sam using SAMtools?
Now, we can use the samtools view command to convert the BAM to SAM so we mere mortals can read it. When you align FASTQ files with all current sequence aligners, the alignments produced are in random order with respect to their position in the reference genome.
How is a binary file different from a SAM file?
This is the same format except that it encoded in binary which means that it is significantly smaller than the SAM files and significantly faster to read, though it is not human legible and needs to be converted to another format (i.e. SAM) in order to make sense to us.
How are SAM / BAM / CRAM files generated?
CRAM/unaligned Bam (uBAM) can be a source of data delivery in some institutions: this cuts down significantly on storage space and transfer speed. How are these files generated? Let’s look at one! The default tool for interacting with these formats is samtools.