Flat plot without any error message

[Yoshihiro]

Hi Li shen,

I'm trying to plot ChIP-seq reads around positions encoded in my bed file.

Following command can work in my PC (Macbook pro 2019). 

However, it did't work in collaborator's computer (OS: Scientific Linux), where we were trying to plot for many bed files sequentially and speedy.

The resulting average plot showed just only flat lines. Heat map was also empty. But there was no error message for running.

Although versions of NGS plot are 2.47.1 in both computers, the same problem was occurred with version 2.63.

 

Command: 

TF=(TF1 TF2 TF3)

for NAME in ${TF[@]}

do

# Prepare configuration file.

touch ${NAME}.txt

echo 'Cell-A_.bam MOTIFNAME_summit.bed "Cell A"'  >> ${NAME}.txt

echo 'Cell-B_.bam MOTIFNAME_summit.bed "Cell B"'  >> ${NAME}.txt

sed s/MOTIFNAME/${NAME}/ ${NAME}.txt > config_motif_${NAME}.txt

#↓

#↓

        # Run NGS plot.

ngs.plot.r -G hg19 -R bed -C config_motif_${NAME}.txt -O output_${NAME}_motif -P 10

done

Thank you for your consideration in the matter.

Thanks,

Yoshihiro

[Etienne Danis]

Hi Yoshihiro,

It could be an issue with the config files.

I would create the config file for one TF and one cell line first and see if it works.

Did the computer of your collaborator have 10 processors since you specified -P 10?

I rarely use sed. The sed line could have an issue.

Instead of using sed, you could just use " " instead of ' '. It will permit you to use $NAME inside the quotation marks.

echo "Cell-A_.bam $NAME_summit.bed "Cell A""  >> ${NAME}.txt

It could help...

Best,

Etienne