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License: GNU General Public License v3.0
JAMM Peak Finder for Sequencing Datasets
License: GNU General Public License v3.0
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?
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
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:123Getting 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
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.
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!
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