read mapping

How do I upload a bigwig file?

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

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.  

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")

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