MAnorm error: unable to open files

Question

[catherine]

I don't if anyone is using MAnorm, or has used it before. But I have some problems with it.

I follow the instruction on README.txt, but get error codes

StepI: clean input

awk: illegal field $(U), name "1"
 input record number 978, file
 source line number 2

StepII: classify common or unique peaks

Error: Unable to open file peak1.bed. Exiting.
....

StepIII: count peak read

Error: The requested file (read1.bed) could not be opened. Error message: (No such file or directory). Exiting!

​Here is my input files info:

​$ls

MAnorm.r MAnorm.sh Rcommand.out peak_R1.bed peak_R2.bed reads_R1.bed reads_R2.bed​

​$head peak_R1.bed 

2L 5521 5964
2L 6597 6868
2L 160815 161069
2L 246781 247069
2L 246781 247069
2L 368765 369063
2L 377759 377966
2L 510702 510866
2L 547280 547428
2L 548129 548278

$head reads_R1.bed 

2L 10620835 10620886 HWI-ST911:217:C4YARACXX:5:1101:1490:1956 255 +
X 9239594 9239645 HWI-ST911:217:C4YARACXX:5:1101:2781:1939 255 -
3L 10851752 10851803 HWI-ST911:217:C4YARACXX:5:1101:3245:1978 255 +
3R 4480617 4480668 HWI-ST911:217:C4YARACXX:5:1101:3361:1999 255 -
3R 23881843 23881894 HWI-ST911:217:C4YARACXX:5:1101:3600:1971 255 +
2R 20832041 20832092 HWI-ST911:217:C4YARACXX:5:1101:3689:1993 255 +
3R 2826772 2826823 HWI-ST911:217:C4YARACXX:5:1101:3571:1996 255 -
3L 6888554 6888605 HWI-ST911:217:C4YARACXX:5:1101:3969:1944 255 -
2L 14067696 14067747 HWI-ST911:217:C4YARACXX:5:1101:3993:1966 255 -
2R 4569412 4569463 HWI-ST911:217:C4YARACXX:5:1101:1388:1967 255 +​

​Any idea why does MAnorm cannot open my file?

Thank you very much!​

Answer 1

[mayuri.rege]

Hi,

I am no expert in MAnorm, but here is what I found in the help file when I was trying to figure out how to use it.

The format for the peaks.bed and the reads.bed file are

chr start end

chr start end strand

To give you a better idea of the format required, here are the help files from the downloaded MAnorm package:

sample1_peaks.bed

chr12    84971385    84976706
chr12    24484005    24487083

sample2_read.bed

chr4    105720192    105720221    +
chr1    173032373    173032415    -

Hope that helps!