This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Erorr in peakannotator

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
• 2,027 views • link
written by Brice222 • Brice222

finally my program shows Number 8

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

• 0 views • link
written by kloetzl kloetzl

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

$ 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 "

• 0 views • link
written by Brice222 • Brice222

0 answers

No answers yet.

Log in to answer this question.

More posts like this