Cisgenome

[doxologist]

http://www.biostat.jhsph.edu/~hji/cisgenome/

Anyone with experience with this software?

If not, what are you using for tiling array, ChIP-seq, genome and cis-regulatory element analysis?

[What_Da_Seq]

Just started using it for MeDIP-CHIP. Import is taking 5h so far (63 .cel files).

[hji]

That's because we process files one by one, and write processed files to hard drive instead of keeping them in the memory. This is for memory considerations. We could design a fast reading procedure (like the old version of tilemap, it reads files much faster than tilemapv2), but that would require you to have memory to bring in all cel files.

[doxologist]

Just started using it for MeDIP-CHIP. Import is taking 5h so far (63 .cel files).

Let us know how you like it...

[What_Da_Seq]

Trying to build the local genome database for mm9 in order to start annotating what I got from the analysis. The CisGenome MM9 annotation file seemed to be missing the refflat.txt files and all other annotation files that are present in the mm8 file
Instructions in the cisgenome manual are definitely outdated and I would greatly appreciate help with the command line interface to build the local database.

Thanks

[doxologist]

We found the instructions a little to follow ourselves... perhaps this is a good suggestion for the CisGenome people.

[What_Da_Seq]

Turns out I do not have to build the database, since the mm9 annotation file has it all (4GB). If you get the following error message "Couldn't open destination file!" you did not edit your .ini file.

[What_Da_Seq]

So far so good. it generates a huge amount of working files and I am still trying to figure out if I need the .mask and .int files for later steps or if I can just delete them after generating .bar files. The annotation and sequence retrieval with their standard files works great too. If i could only figure out how to format the mm9 miRNA reference file for annotation that would be nice. Oh yes if they incorporate BS-seq and RRBS-seq we would be in perfect business.
I will let you know how the validation of some of these MeCpGs is coming along or if I am just looking at statistical noise (cross my fingers).

[comingme]

hts_windowsummaryv2_2sample and I get
Error: Affy_LoadBAR, cannot open *.bar file

however I can use affy_bar2txt to convert bar to text file.
Do not know what happened.

[alere]

I'm trying to download the Hg18 Genome database for cisgenome but seems that the website is stuck!!
Anyone has this problem??
thanks

[Bioinfo]

hi
Do anyone had worked on chipseq analysis at CisGenome(Windows GUI).
However I am able to convert "bed" to "aln" and then alignment to BAR files. The exploration steps seems not working for me. I dont know what wrong with me and no error message as well.
Greatly appreciate any help
thanks.

[didye]

@comingme :
I got the same problem on my Bar data file.
Did you fix it?
Regards

[ajaffe]

@ didye
I was having the same problems with reading in my ChIP-chip bar files, but the problem was fixed when I correctly specified my probe model. I used one of the precompiled ones that was available for my Mouse Promoter array on the CisGenome website

[gntc]

cisgenome complaints

I have found using Cisgenome to be a very unpleasant experience. The Users Manual is very brief and often does not explain clearly how to use each program, what the program is doing, and what the output means. Error reporting within the program itself is abysmal. If something goes wrong the program dies and does not display to the user that there was even a problem, let alone what the problem was. Errors are often simple things such as I forgot to specify an output directory, but it is frustrating when the program dies and doesn't explain why. I emailed the developers with my problems and they sent me back one brief reply with no new information and were of no further help. Once I finally figured out how to run the program I found it to be slow and annoying to use. If you can find another program that suits your needs I would recommend using that.