There are at least 4 programs/scripts that are needed to convert a bam to a bigwig file from a standard read mapping bam file. 2 of these are non-standard and will probably need to be downloaded, but are very simple to use and install.
#bioawk can be had from github here https://github.com/lh3/bioawk. The installation is a breeze: gunzip, cd directory, make.
Tabix is a program that is necessary to be able to index the vcf file for upload and display in Jbrowse. Once this program is installed, the process is fairly easy.
Be aware that your scaffold names must match the Jbrowse scaffold names in every respect (capitalization, underscores, numbering, etc). Also, the vcf does not necessarily need to be sorted, which is different from all other file types.
1. Zip your file with bgzip. As simple as "bgzip file.vcf"
3. Index your zipped file with tabix. "tabix -p vcf file.vcf.gz"
First thing to consider, is your bam file larger than 10Gb? 10Gb is the maximum allowable file size to upload to SCNbase, and thus you will not be able to make it publicly available. However, files that are larger than 10Gb can be viewed by directly uploading them to Jbrowse, rather than SCNbase.
1. Map your reads to the genome. Make sure it is the correct version of the genome found here on SCNbase.org, "genome738sl.polished.mitoFixed.fa"
2. Convert your sam file to a bam file (Can be done with "samtools view -bS file.sam >file.bam")
Tabix is a program that is necessary to be able to index the gff file for upload and display in Jbrowse. However, getting a gff file viewable in jbrowse is a little more work than a bed file.
1. Sort your gff file by scaffold name and position. Typically this works like "sort -k1,1V -k4,5n file.gff >sorted_file.gff"
2. Zip your file with bgzip. As simple as "bgzip sorted_file.gff"
3. Index your zipped file with tabix. "tabix -p gff sorted_file.gff.gz"
Tabix is a program that is necessary to be able to index the bed file for upload and display in Jbrowse. Once this program is installed, the process is fairly easy.
1. Sort your bed file by scaffold name and position. Typically this works like "sort -k1,1V -k2,2n bedfile.bed >sorted_bedfile.bed"
2. Zip your file with bgzip. As simple as "bgzip sorted_bedfile.bed"
3. Index your zipped file with tabix. "tabix -p bed sorted_bedfile.bed.gz"
A data curator has expertise in bioinformatics or experience with GMOD tools and JBrowse. The fastest way to get your data loaded into SCNBase is for a member of each group to familiarize themselves with standard file upload forms. For more complex training to ensure this community grows, contact Andrew Severin.
Data can be downloaded using the Downloads link on the homepage. All data and corresponding metadata currently available in SCNBase is available here.
Use the search bar to narrow down the data your search for the data you wish to download.
