clipper wont run on bacterial genome

[Tsviya Olender]

Hi
I am trying to follow the wiki and run Clipper on bacterial Clip-Seq data. I tried:
[lvzvia@molgen Sarit_Tsviya]$ python /home/labs/olenderlab/lvzvia/MySoftware/clipper-master/clipper/src/peakfinder.py -b alignment/m6A_2_10_AB_S8.U.bam --customBED genomeT/m6A_2_10_AB_S8.peaks.bed
Usage:
python peakfinder.py -b <bamfile> -s <hg18/hg19/mm9>
 OR

python peakfinder.py -b <bamfile> --customBED <BEDfile> --customMRNA
    <mRNA lengths> --customPREMRNA <premRNA lengths>

peakfinder.py: error: no such option: --customBED

so I have tried:
[lvzvia@molgen Sarit_Tsviya]$ python /home/labs/olenderlab/lvzvia/MySoftware/clipper-master/clipper/src/peakfinder.py -b alignment/m6A_2_10_AB_S8.U.bam --bedFile genomeT/m6A_2_10_AB_S8.peaks.bed
Usage:
python peakfinder.py -b <bamfile> -s <hg18/hg19/mm9>
 OR

python peakfinder.py -b <bamfile> --customBED <BEDfile> --customMRNA
    <mRNA lengths> --customPREMRNA <premRNA lengths>

peakfinder.py: error: no such option: --bedFile

and also
[lvzvia@molgen Sarit_Tsviya]$ clipper -b alignment/m6A_2_10_AB_S8.U.bam --bedFile genomeT/m6A_2_10_AB_S8.peaks.bed
Usage:
python peakfinder.py -b <bamfile> -s <hg18/hg19/mm9>
 OR

python peakfinder.py -b <bamfile> --customBED <BEDfile> --customMRNA
    <mRNA lengths> --customPREMRNA <premRNA lengths>

clipper: error: no such option: --bedFile


How should I use it?

Tsviya

[Jie Wu]

I got the same problem. Most of the parameters in clipper are not useful. And they hardly reply to questions here. I guess clipper is not maintained.  

在 2017年5月18日星期四 UTC+2下午2:01:43，Tsviya Olender写道：