On 27 April 2010 15:23, Brad Chapman
<chapmanb@50mail.com> wrote:
Claudia;
> I am trying to use MACS among your NGS peak-calling tools, but I
> can't work it out.
>
> I have ELAND files; what should I specify as a file
> format when uploading them? There is no ELAND format in the 'upload file'
> window. If I choose BED as a format, after running MACS I get no results
> (empty) and a Strand Format Error message, although I am sure the strand
> information in my ELAND file is correct (9th column, F or R). If I choose
> TABULAR, instead, my files are not even visualized in the MACS dropdown
> menu.
>
> Is this a problem of input file format, as I suspect?
I don't make much direct experience with Eland format, but have
not seen support for it in Galaxy. My suggestion would be to
convert your Eland output into BED, and then proceed. Taking a
quick look, here is one perl script that may work for you:
http://www.pangloss.com/wiki/Solexa/ElandExport2BED
Hope this helps,
Brad