Homer for NGS analysis

Question

[Azhar]

I Just started chip seq analysis using Homer, is there any body used it before who can help me because I am facing some errors at every step and some times I cant understand them

[Sean Davis]

Welcome to Biostars. Biostars works as a question/answer forum. The only way to get meaningful help here is to ask a question that can be answered online. In other words, if you are having questions about software (homer), please provide enough detail to allow us to try to answer. For example, include the command line you tried to execute and the error message you received. It is also a good idea to try to include enough information that someone could reproduce your problem (such as software versions, running on example data). Start by editing this question to include more detail.

[Azhar]

I have a file of 3.27 Gb chip seq and bowtie align file is 5.04 GB some one told me that sam output file.sam is not so big, I want to ask that whether I am in right direction?

[Sean Davis]

This is not the type of help that lends itself to biostars. Please ask a SPECIFIC question. Unfortunately, we cannot really tell you if you are headed in the right direction without a great deal more specifics. I would suggest that you find a collaborator with whom you can work closely to get things started.

[Fidel]

Have you tried deepTools? There is a galaxy instance that you can use for your analysis and an extensive documentation.

[Azhar]

No I am using Homer, now I am going to build data visualization graph using bed tools but I have some confusion

I have two files one is outputPrefix.bam and second is outputPrefix.bam.bai, the second one is sorted but bedtools genomcov -i option demand file that end with bam I don't know what to do

Can somebody send me bedtools genomecov command with some explanation

Thanks