I am new in using the IGB, now i have two questions.
First,I want to visualize the ChIP-seq data through IGB .its ok to load the genome and bed file, but when i open the bam file, it always note me "Region in view is big(>500k),do you want to continue?" .after click ok ,there is still no data for the bam file. what should I do to visualize the bam file ??
Second, when I want to load the genome sequence, it always fails, but my internet is good and the speed is ok, why I cannot load the sequence successfully?
thanks a lot for your reply.
Do you run the IGB as webstart or locally? In case of webstart use as much RAM as possible, otherwise run it from the commandline as suggested here and provide 8 to 10 G.
You can download the annotation here just browse to your genome. Usually, it's given in FASTA format. Eventually, each chromosome is in a different file. You should concatenate them in the same order as in given order in the bam-header (samtools view -H my.bam).
I run the IGB as webstart, got it and thank you very much!