Erorr in peakannotator

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7.5 years ago

Brice222 ▴ 30

Hello all.

I have a Chip-Seq data. I ran Bowtie2 and MACS2 on that data. I got peak files like name.bed. Right now to annotate that peaks , I am using PeakAnnotator software. I downloaded annotation from Ensembl .(ftp://ftp.ensembl.org/pub/grch37/release-89/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz) But when Iam runnig Peakannotator (https://www.ebi.ac.uk/sites/ebi.ac.uk/files/groups/bertone/software/PeakAnnotator_Java_README) , finally my program shows Number 8, then the running of Peakannotator is stoped.

Thanks a lot

ChIP-Seq annotation software error next-gen • 1.6k views

ADD COMMENT • link 7.5 years ago by Brice222 ▴ 30

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finally my program shows Number 8

Please paste the whole error message. This is not much to go on.

ADD REPLY • link 7.5 years ago by kloetzl ★ 1.1k

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Exactly. In addition, also add the exact commands you used to run Bowtie2, MACS2 and Peakannotator.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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$ java -jar peakAnnotator.jar -u NDG -p Srr83_PeakCall_peaks.bed -a Homo_sapiens.GRCh37.87.gtf -o /home/Annotat -x Srr83_Anno

After running the command Error seen below.

" Starting...

Reading Homo_sapiens.GRCh37.87.gtf file

8 "

ADD REPLY • link 7.5 years ago by Brice222 ▴ 30

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