NGS software tips: SICER for ChIP-seq
Tip: Do NOT need to move SICER anymore.
For SICER, if you are going to the original code, you have to copy the source code to your working directory.
This is because the PATHTO variable varies when you’re doing different work.
To avoid this, you can modify the code to:
PATHTO="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
#SICER=$PATHTO/SICER
SICER=$PATHTO
PYTHONPATH=$SICER/lib
export PYTHONPATH
Tip: About duplicate reads
One step of SICER is to remove duplicate read using remove_redundant_reads.py. “-t 1” is the default cutoff when doing duplicate reads removal. See line 60 of remove_redundant_reads.py.
Solved: Error Report.
File "/depot/bioinfo/Projects/Kal/bean_GHvsTC/software/SICER_V1.1/SICER/src/remove_redundant_reads.py", line 84
print chrom, "\tPlus reads:",p_total, "\tRetained plus reads:", p_retained, ";\tMinus reads:", m_total, "\tRetained minus reads:", m_retained;
^
print chrom, "\tPlus reads:",p_total, "\tRetained plus reads:", p_retained, ";\tMinus reads:", m_total, "\tRetained minus reads:", m_retained;
^
The reason is I used a higher version of python (Python 3.4.3 :: Anaconda 2.2.0 (64-bit)) which is the default version I usually use. If I used a lower version (Python 2.7.10 :: Anaconda 2.0.1 (64-bit). Maybe this is because there are some problems related to compatibility between the python and the packages we used in SICER.
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