file

How do I upload a vcf file?

Abbreviated Question: 
How do I upload a vcf file?
Answer: 

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"

How do I upload a bam file?

Abbreviated Question: 
How do I upload a bam file?
Answer: 

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")

How do I upload a gff file?

Abbreviated Question: 
How do I upload a gff file?
Answer: 

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"

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