Entering edit mode
9.0 years ago
Azhar
▴
50
hi friends
I have a bam files and I can want to view it into ucsc browser, I have to just upload into custom track option or edit it by custom track line and what is meant by bam and bai files
Please be clear in asking questions. If you have more than one question make sure they are well separated so that readers can understand them. For custom track display, both the BAM file (.bam) and its associated index file (.bai) should be uploaded to a web-accessible server (http, https, or ftp), and the public link should be mentioned in the custom track. Samtools can be used to create ".bai" file from bam file. To know more check the following link: http://genome.ucsc.edu/goldenpath/help/bam.html
My question is bam file is sorted file and bai is indexed file now these are both in same dirc, now what is public link would be? And second is my file is about 1.31GB is its size is ok? Or simply I have to just browse and upload file in custom track option or have to give trackline in custom track and what kind of that track line would be
You need to upload the bam file to server that is publicly accessible. You will have to mention the public link or url in the custom track. See this post: a question about sharing the ucsc custom track to other people
Brother I have a bam file of 1.31 gb I don't know how to upload that because it gives error, and some body told me you just have to browse and upload file in ucsc browser but it needs to be less then 50mb is it right or not. Please I need urgent help
The file is too big. You may need a local genome browser. For example, IGV https://www.broadinstitute.org/igv/