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4ureliek / TEanalysis

Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.
MIT License
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TE-analysis_Shuffle_bed.pl errors #1

Closed JinfengChen closed 8 years ago

JinfengChen commented 8 years ago

Hi Aurelie, I am playing with TE-analysis_Shuffle_bed.pl to test enrichment of TE in chip seq peaks. The script report errors "WARN: no value for total number (from RM output), for {age}{cat.1}{tot}? => no binomial test". I checked the result file "H3K4me3_peaks.1.bed.boot.age1" and found one column is empty. I shared my input files to you (https://github.com/JinfengChen/TE_analysis/blob/master/test.tar.gz). Can you please take a look and help with the input format? Thanks.

Jinfeng

File with empty column: H3K4me3_peaks.1.bed.boot.age1 boot.1 age cat.1 tot 31562 31562 20014 boot.2 age cat.1 tot 31562 31562 1989

command line: perl ./Utils/TE-analysis_Shuffle_bed.pl -f H3K4me3_peaks.1.bed -s MSU_r7.fa.RepeatMasker.class.nonTE-none.bed -r MSU_r7.fa.build.tab -e MSU_r7.fa.gaps.bed -n 10

4ureliek commented 8 years ago

Hi, The age categories should only be considered if a file with the age info for the TEs is provided with -g,--group. You can ignore this error and look at the rest of the results - it should not be a die/kill error. I will update shortly a fixed version. Cheers, Aurelie

4ureliek commented 8 years ago

I updated a fixed version - please let me know if you still get errors!

JinfengChen commented 8 years ago

Thanks, Aurelie. I updated the script and it works fine now. I found out the cause of my failure is the version of Statistics::R. I used 0.2 but 0.34 is the right version. Best.

Jinfeng

On Nov 3, 2016, at 12:52 PM, Aurelie Kapusta notifications@github.com wrote:

I updated a fixed version - please let me know if you still get errors!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/4ureliek/TEanalysis/issues/1#issuecomment-258254950, or mute the thread https://github.com/notifications/unsubscribe-auth/AELguO5pVCdsgUKFsXG34CzZ6WIIc_Ccks5q6juYgaJpZM4Kov5q.