No output and no visualization with

[Gy. A]

Dear All,

I've installed RSEQC under Ubuntu 14.04. Also, I believe I have installed all the required softwares, like: python 2.7 , pysam 0.7   cython, etc. Also Ive installed rseqc  with the python setup.py install command. I also installed R via sudo apt-get.

However, when I try to use the read-distribution.py program, it does not generate any output file, or at least I can not find it. After running the script, it writes that it is processing the bed file ( reference ) but nothing else, and then quits. Without output.

Could you please tell were should I expect the output file? And otherwise what other details could I have missed?

Thank you for the help, and I wish all the best,

Best

Akos

[Liguo Wang]

read_distribution.py will output some thing like this:

Group	Total_bases	Tag_count	Tags/Kb
CDS_Exons	33302033	20002271	600.63
5’UTR_Exons	21717577	4408991	203.01
3’UTR_Exons	15347845	3643326	237.38
Introns	1132597354	6325392	5.58
TSS_up_1kb	17957047	215331	11.99
TSS_up_5kb	81621382	392296	4.81
TSS_up_10kb	149730983	769231	5.14
TES_down_1kb	18298543	266161	14.55
TES_down_5kb	78900674	729997	9.25
TES_down_10kb	140361190	896882	6.39

See our online manual for details:
http://rseqc.sourceforge.net/#read-distribution-py

Please also check if the chromsome IDs ("chr1", "chr2",..., "chrX", etc) are matched between your BED file and your BAM file.

Liguo

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