Open kwonej0617 opened 1 year ago
Curious. I'm not sure what has happened here. Would you be able to show the full commands used for both and also confirm that you are running both in transcriptome mode? Did you see any errors reported during the analysis?
Actually, I used the same command line for both samples. Also, none of the errors occurred. python DRUMMER.py -r ${ref} -l ${txt} -t ${ko_bam} -c ${wt_bam} -o sample1/com -m True -a isoform python DRUMMER.py -r ${ref} -l ${txt} -t ${ko_bam} -c ${wt_bam} -o sample2/com -m True -a isoform
Between those two cases, which one is the correct one?
data/output/DRUMMER/sample1/com/w-k: #no gTEST and MERGED directories generated
bam_readcount complete_analysis map m6A_plot.pdf summary.txt
data/output/DRUMMER/sample2/com/w-k: #no m6A_plot.pdf generated, no files in MTOIF and ODDS directories bam_readcount complete_analysis gTEST map MERGED MOTIF ODDS summary.txt
Also, I have another question. I was wondering if you have deposited meRIP-seq data of adenovirus in supplementary data. Is it the one in Ad5 viral m6A peaks tab in supplementary data2?
Thank you for your help!
Hello, Thank you for developing a great tool. I have run DRUMMER with my data and obtained several output folders. I used the same command line for DRUMMERS for both sample 1 and sample 2. However, the output files and directories generated from the two data are different. Could you please check if one of the data has not been processed completely?
data/output/DRUMMER/sample1/com/w-k: #no gTEST and MERGED directories generated bam_readcount complete_analysis map m6A_plot.pdf summary.txt
data/output/DRUMMER/sample2/com/w-k: #_no m6Aplot.pdf generated, no files in MTOIF and ODDS directories bam_readcount complete_analysis gTEST map MERGED MOTIF ODDS summary.txt
The outputs are quite different between the two data, but the final summary.txt. files look successfully generated. Summary.txt from sample 1
Summary.txt for sample 2