What does samtools view do?

The samtools view command is the most versatile tool in the samtools package. It’s main function, not surprisingly, is to allow you to convert the binary (i.e., easy for the computer to read and process) alignments in the BAM file view to text-based SAM alignments that are easy for humans to read and process.

How do I view a BAM file?

BAM files can be opened from remote locations (ftp, http) and from local computers. 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.

How does a SAM file look like?

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.

What does samtools Fixmate do?

The samtools fixmate tool corrects any flaws in read-pairing that may have been introduced by the aligner.

How do I view a Quickq file?

I-1 Exploring FASTQ files in UNIX.

1. Login to the server, as you learned from Day 1, using.
2. Create a symbolic link to the directory containing the input files, and add PATH $ ln -s /home/hmkang/bioboot/data/ data.
3. Examine the contents of the FASTQ files $ zless data/bioboot_2015a_R2.fastq.gz.

What is BAM index?

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. Indexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention.

How do I view BAM in IGV?

Visualizing a BED, BAM or GTF file from a URL In IGV, select File > Load from URL … A window will pop up and ask you to give the correct URL for the file you want to view. Paste in the URL and the file will be downloaded. From the file extension, IGV will automatically treat the information in the file accordingly.

What is BAM format?

A BAM file (*. 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. …

What is a SAM file in Windows?

The Security Account Manager (SAM) is a database that is present on computers running Windows operating systems that stores user accounts and security descriptors for users on the local computer. SAM objects include the following: SAM_ALIAS: A local group.

Where is the SAM file in Windows 10?

C:\Windows\System32\config
These hashes are stored in the Windows SAM file. This file is located on your system at C:\Windows\System32\config but is not accessible while the operating system is booted up.

What is Fixmate?

Augmented reality remote assistance. Fixmate enables peer-to- peer virtual communication and interaction through digital marks on your video calls with your peers/customers. You can measure anything on a real-time video call.

Does SAMtools work on Windows?

We managed to compile samtools 1.1 on Windows (64 bit). Most of the functionality works. If you are interested, omnomicsQ contains compiled samtools which you can use. A registration for a free trial is needed.

What is the basic usage of the SAMtools view?

The basic usage of the samtools view is: where input_alignments. [bam|sam] is the input file with the alignments in BAM/SAM format, and output_alignments. [sam|bam] file is the converted file into SAM or BAM format respectively.

Do you need an index file for SAMtools?

If the header information is available: Always sort your BAM files; many downstream programs only take sorted BAM files. Like many Unix tools, SAMTools is able to read directly from a stream i.e. stdout. A BAM index file is usually needed when visualising a BAM file.

What to do with BAM files in SAMtools?

If you run samtools on the terminal without any parameters, all the available utilities are listed: Most of the times I just use view, sort, index and flagstats. A BAM file is just a SAM file but stored in binary; you should always convert your SAM files into BAM to save storage space and BAM files are faster to manipulate.

What to do if the header is not available in SAMtools?

If the header is absent from the SAM file use the command below, where reference.fa is the reference fasta file used to map the reads: If the header information is available: Always sort your BAM files; many downstream programs only take sorted BAM files. Like many Unix tools, SAMTools is able to read directly from a stream i.e. stdout.