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What Is the Main Difference Between a Sam or Sam File Format and a Bam or Bam File Format?

FAQs Jackson Bowman September 14, 2022

SAM files are human-readable text files and BAM files are simply their binary equivalent, while CRAM files are a restructured columnar binary container format. BAM files are typically compressed and more efficient for software than SAM.

What is the difference between SAM and BAM file format?

BAM files contain the same information as SAM files, except they are in binary file format, which is not human readable. On the other hand, BAM files are smaller and more efficient for software than SAM files, saving time and reducing computation and storage costs.

What is SAM file and BAM?

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 analyzed and edited using the SAMtools software.

What is BAM file used for?

A BAM file (*.bam) is the compressed binary version of a SAM file used to represent aligned sequences up to 128MB.

What is BAM file format?

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. These formats are described on the SAM Tools website: http://samtools.github.io/hts-specs/.

What is the SAM file?

What is Security Accounts Manager (SAM)? The Security Accounts Manager (SAM) is a database file in the Microsoft Windows operating system (OS) that contains usernames and passwords. The main purpose of the SAM is to make the system more secure and protect against data breach in case the system is stolen.

What is a SAM file and how is a SAM file generated?

What is SAM. The SAM format is a text format for storing sequence data in a series of tab-delimited ASCII columns. It is mostly generated as a human-readable version of its sister format, BAM, which stores the same data in a compressed, indexed, binary form.

What are BAM files RNA seq?

BAM is a binary, compressed version of the SAM file, also known as the Sequence Alignment Map format. The introduced SAM file is a tab-delimited text file that contains information for each individual read and its orientation to the genome.

Are BAM files smaller than SAM?

For almost any application that requires SAM input, this can be generated on-the-fly from a BAM file (using ‘samtools view reads.bam |’). BAM files take up much less disk space than SAM files.

Where is SAM file stored?

The SAM database is stored in two locations within Windows: %systemroot%\system32\config\sam is the location of the main store for passwords and %systemroot%\repair\sam. _ is a backup of the main file in case it needs to be restored for a repair operation.

How many reads in BAM file?

391696 is the number of mapped alignments in the BAM file. This includes multimappers, so it doesn’t necessarily have to be the number of reads mapped. This is identical to above and does exactly the same thing. This is the number of entries in a pair, excluding those marked Read #1.

How do I create a BAM file?

How do you visualize a BAM file?

Visualize a BED, BAM, or GTF file from a URL

In IGV, select File > Load from URL … A window will open asking you to enter the correct URL for the file to be displayed. Paste the URL and the file will download. Based on the file extension, IGV automatically handles the information in the file accordingly.

Are BAM files compressed?

The BAM format was a huge success due to its ability to compress aligned reads by about 50-80% of their original size, but even that is not sustainable in the long run.

What is the difference between a SAM database and an Active Directory database?

An account database maintains the security principals and necessary information for authentication and other purposes. On Windows, an Active Directory database manages domain security principals, while the built-in Security Account Manager (SAM) database manages local security principals.

What should a SAM file look like?

SAM files are TSV (tab-separated-values) files and start with an optional header. The header consists of several lines starting with an ‘@’ sign, each line is a record. Each record begins with its identifier, followed by tab-delimited tags.

What is SAM name in Active Directory?

The Security Account Manager (SAM) is a database file in Windows XP, Windows Vista, Windows 7, 8.1, 10 and 11 that stores users’ passwords. It can be used to authenticate local and remote users. Beginning with Windows 2000 SP4, Active Directory authenticates remote users.

How is SAM file generated?

SAM format

Generated by almost every existing alignment algorithm. It consists of a header, a row for each read in your record, and 11 tab-delimited fields that describe that read.

References:

  1. https://www.zymoresearch.com/blogs/blog/what-are-sam-and-bam-files
  2. https://en.wikipedia.org/wiki/SAM_(file_format)
  3. https://support.illumina.com/help/BS_App_RNASeq_Alignment_OLH_1000000006112/Content/Source/Informatics/BAM-Format.htm
  4. https://software.broadinstitute.org/software/igv/BAM
  5. https://www.techtarget.com/searchenterprisedesktop/definition/Security-Accounts-Manager
  6. https://genome.sph.umich.edu/wiki/SAM
  7. https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/04_alignment_quality.html
  8. http://barcwiki.wi.mit.edu/wiki/SOPs/miningSAMBAM
  9. https://www.sciencedirect.com/topics/computer-science/security-accounts-manager-database
  10. https://www.biostars.org/p/138116/
  11. https://www.youtube.com/watch?v=NMhLA5gFhRE
  12. https://scilifelab.github.io/courses/rnaseq/labs/IGV
  13. https://www.uppmax.uu.se/support/user-guides/using-cram-to-compress-bam-files/
  14. https://docs.microsoft.com/en-us/openspecs/windows_protocols/ms-authsod/523ed32c-3a6c-4a3d-b50b-bb99e321c2eb
  15. https://seqan.readthedocs.io/en/seqan-v1.4.2/Tutorial/BasicSamBamIO.html
  16. https://en.wikipedia.org/wiki/Security_Account_Manager
  17. https://learn.gencore.bio.nyu.edu/ngs-file-formats/sambam-format/

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