BSeQC_RPKM

[Xueqiu Lin]

Hi,

I try to run RPKM_saturation.py, the command is RPKM_saturation.py -i accepted_hits.bam -o WT_rep1_accepted_hits_rpkm_saturation -r RSeQC/mm9_NCBI37_Refseq.bed

The BAM file is paired-end, and from tophat mapping.

And I have met a error:

Traceback (most recent call last):

  File "/home/xueqiul/anaconda/bin/RPKM_saturation.py", line 5, in <module>

    pkg_resources.run_script('RSeQC==2.3.9', 'RPKM_saturation.py')

  File "/home/xueqiul/anaconda/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg/pkg_resources.py", line 461, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/home/xueqiul/anaconda/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg/pkg_resources.py", line 1194, in run_script

    execfile(script_filename, namespace, namespace)

  File "/home/xueqiul/anaconda/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/RPKM_saturation.py", line 172, in <module>

    main()

  File "/home/xueqiul/anaconda/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/RPKM_saturation.py", line 159, in main

    show_saturation(infile=options.output_prefix + ".eRPKM.xls", outfile=options.output_prefix + ".saturation.r",rpkm_cut = options.rpkm_cutoff)

  File "/home/xueqiul/anaconda/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/RPKM_saturation.py", line 118, in show_saturation

    norm_RPKM[head[i]].append(str(j))

IndexError: list index out of range

Thanks,

Xueqiu

[Liguo Wang]

in your WT_rep1_accepted_hits_rpkm_saturation.eRPKM.xls file, do you see a header line starting with '#'?  Thanks.

Liguo

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[XueqiuLin]

I just  see one header line:

#chr start end name score strand 5% 10% 15% 20% 25% 30% 35% 40% 45% 50% 55% 60% 65% 70% 75% 80% 85% 90% 95% 100%

Thanks,

Xueqiu

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[Liguo Wang]

Then it really confused me. Maybe this file is damaged, you could check if the file "WT_rep1_accepted_hits_rpkm_saturation.eRPKM.xls" has the same number of columns for each row. You already get the results, but the error you had is about visualization.

Or you simply rerun it.

Thanks

Liguo

[XueqiuLin]

There are 3 rows which have 46 columns, while the others have 26. 

And I have got the same output when I rerun it.

Thanks,

Xueiqu

[Liguo Wang]

If  concatenation of  the first 6 columns (chrom, start, end, name, score, strand) of each bed entry can NOT make it unique, you would encounter such error.  The temporary solution is remove such duplicate entries from your BED file.

We will fix this bug.

Thanks

Liguo