mahmoudibrahim/jamm

JAMM Peak Finder for Sequencing Datasets

jamm's Issues

Add build system

Currently, this package lacks a build system and makes assumptions about the location of installed scripts and dependencies at runtime.

Would you be interested in patches to add Autotools support?

How to exclude chromsomes/small contigs

Hi Mahmoud,

currently, I am testing JAMM on GRO-seq (SE protocol, Pol2 ChIP-like pattern) in dm6. This genome version contains a lot of small contigs, which I'd like to ignore/exclude from being analyzed. Thus, muy question, how can I tell JAMM to ignore chromosomes or which data do I need to filter (BED, genome_file)?

Cheers,
-Michael

PS: Sorry, if I missed in the documentation

Cant generate peak files

Hi Mahmoud,

I ran the command bash JAMM/JAMM.sh -s Sample/ -g hg38.size -o Output -c Control/
I got outputs shifts.txt, xcorrsummary.txt, xcorrsummary.pdf but not the peaks.

Loading genome size file...Done!
Processing sample files...
Done!
Processing control files...
Done!
Getting average read lengths...
Control: 122
ChIP_rep2_K_35Mileach_merge: 122
Calculating Fragment Length(s)...
chr1, ChIP_rep2_K_35Mileach_merge: Ok!
chr1, ctrl: Ok!
chr10, ChIP_rep2_K_35Mileach_merge: Ok!
chr10, ctrl: Ok!
......

Then error messages like the following for every chromosome when calling peaks

chrY_KI270740v1_random: No reads found in one or more replicates!
@/fml/obi/data/Dingwen/PeakCallingComparison/Output_K/xcorr/ChIP_rep2_K_35Mileach_merge/shifts.txt
Fragment Length:123

@/fml/obi/data/Dingwen/PeakCallingComparison/Output_K/xcorr/ctrl/shifts.txt
Fragment Length:123

Getting Bin Size: 61
Calling Peaks...(mode: normal, resolution: peak)
Chromosome chr1: Error in switch(EXPR = modelName, X = , E = , V = , XII = , XXI = , XXX = , :
EXPR must be a length 1 vector
Calls: initparam -> mclapply -> lapply -> FUN -> me -> checkModelName
Execution halted
Chromosome chr10: Error in switch(EXPR = modelName, X = , E = , V = , XII = , XXI = , XXX = , :
EXPR must be a length 1 vector
Calls: initparam -> mclapply -> lapply -> FUN -> me -> checkModelName
Execution halted

Also in the end no peaks were generated.

cat: 'Output/peaks/*.bed': No such file or directory
No Peaks Found!

Thanks in advance,
Dingwen

JAMM cannot locate bed or bedpe files even though they are present.

Hello
I am using JAMM v1.0.7.6. I created the .bedpe files using bedtools -bedpe and my source bamfiles.
I want to use to call peaks in paired end mode. It does not recognise the -t parameter in the command line and keeps looking for .bed files when I have provided bedpe.
If I coerce the default to paired-end mode, it cannot locate the .bedpe in the sample folder provided. Is this a known issue or am I doing something wrong?
My commands are :
for the paired-end:
~/sources/JAMM-JAMMv1.0.7.6/JAMM.sh -t 'paired' -s JMJD3_bedpe -c JMJD3_sham_bedpe -g ~/sources/JAMM-JAMMv1.0.7.6/rn6.chrom.sizes -p 5 -T ./temp -o JMJD3_JAMM_peakmode

I just edited the JAMM.sh where the default is changed to paired and saved it as another copy with the same command as above. The error persists that it cannot find .bedpe or .bed files when the files are clearly present.

mclust library issue

I ran the JAMM.sh successfully before but now that I am trying to run the same script I get the following error:
Calls: initparam ... lapply -> FUN -> me -> eval -> eval -> meV -> .Fortran
Execution halted

I updated mclust package and it didn't work.
How can I resolve this issue?

Thanks!