different file formats for ucsc genome browser

Parameters for BAM custom track definition linesĪll options are placed in a single line separated by spaces. Paste the custom track line into the text box in theĬustom track management page, click submit Track type=bam name='My BAM' bigDataUrl= Īgain, in addition to, the associated index file 'track' line will look something like this: Will need to create a track line, as shown below in If you want to configure the track name and descriptions or the URLs are not as described, you The track name will then be the name of the file. URL directly into the custom track management page,Ĭlick submit and view in the Genome Browser. bam and the BAM index file URL ends with. This keyword is relevant in Custom TracksĪnd Track Hubs. bam.bai index file with the bigDataIndex keyword. Hosting site does not use the filename as the URL link, you will have to specificallyĬall the location of this. Looks for an index file with the same URL as the BAM file with the. Move both the BAM file and index file ( my.sorted.bam and New file, my., with which genomic coordinates can quickly be translated

bam to my.sorted, creating a BAM file ofĪlignments ordered by leftmost position on the reference assembly. For more information about the command, run If converting a SAM file that does not have a proper header, the -t or Samtools, please contact the SAM tools mailing list.Īlign sequences using a tool that outputs SAM directly, or outputs a format that can be convertedĬonvert SAM to BAM using the samtools program:

No command line arguments it should print a brief usage message. Test your installation by running samtools with If you haven't done so already, download and build the samtools program. The typical workflow for generating a BAM custom track is this: If you do not have access to a web-accessible server and need hosting space for your BAMįiles, please see the Hosting section of the Track Hub UCSC temporarily caches the accessed portions of the files to speed up interactiveĭisplay. Both the BAM file and itsĪssociated index file remain on your web-accessible server (http, https, or ftp), not on the UCSC To UCSC would time out when attempting to upload the whole file to UCSC. This makes it possible to display alignments from files that are so large that the connection Is that only the portions of the files needed to display a particular region are transferred to Track display, the main advantage of indexed BAM over PSL and other human-readable alignment formats Many next-generation sequencing and analysis tools work with SAM/BAM. BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of

Different file formats for ucsc genome browser