findPeaks in homer
I'm a computer engineer and not very familiar with the Homer tool, I studied homer but I do not know what causes the low error?
findPeaks Sox2-ChIP-Seq -style factor -o auto
error-->findPeaks: command not found
chip-seq
homer
findpeaks
• 2,590 views
•
link
updated
by
Ram
4.5K
• |
written
by
mohamadrezakeshtkar
0
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
findPeaks in homer
written by mohamadrezakeshtkar 0I'm a computer engineer and not very familiar with the Homer tool, I studied homer but I do not know what causes the low error? …
-
Can't find documentation about output of homer2 find command
written by colin.kern 117I have a set of short sequences obtained from doing DNase footprinting and I want to filter them by removing sequences that don't contain a …
-
homer IDR, pseudoreplicates error
written by boczniak767 89Hi all, I'm trying the IDR procedure for FAIRE-seq peaks generated with Homer The procedure is outlined here [homer-idr][1] [1]: https://github.com/karmel/homer-idr#using-homer-idr It works ok till …
-
HOMER tss command not working
written by carlee.bettler 1Hi, I'm new to working with HOMER and I'm trying to find binding at transcription start sites for mouse genome mm9 Chip-Seq data. Based on …
-
HOMER tagInfo metrics for ATAC-seq
written by shankasal 1I'm trying to make sense of all of the parts of the tagInfo.txt metrics that HOMER spits out during makeTagDirectory for a sam file from …
-
can I use homer findpeaks -style dnase to analyse Faire-seq file?
written by Ming Lu 3can I use homer findpeaks -style dnase to analyse Faire-seq file? or which style is better or no style suite for Faire analysis? just in …
-
Homer motif analysis: "Very close % of target vs % of Background sequences with Motif" & "SeqBias a…
written by chiefcat 18Hi everyone. I'm trying to find the motifs bound by my ChIP-ed protein using Homer. I don't have knowledge regarding NGS analysis. The analysis was …
-
Visualize smooth ChIP peaks with Homer makeUCSCfile
written by varsha619 9Hello, I am trying to use Homer makeUCSCfile for my ChIP seq data using as follows - makeUCSCfile sample.tagdir/ auto -style chipseq > sample.bedGraph.gz Although …
-
Doubt in using Homer: annotatePeaks.pl in TSS mode
written by k.balaji93 1So I am using HOMER to get differentially expressed peaks across 2 treatment groups, with 2 replicates each (say t1_1, t1_2 and t2_1, t2_2). I …
-
What Parameters Do You Use With Findpeaks For Chip Seq Peak Calling?
written by Stew 143<p>I would like to use FindPeaks to call peaks on chIP-seq data, where I have an IP against a sequence specific transcription factor, using Input …
Please be more careful while creating posts - this is a
Questiontype post and not aTooltype post. I've made the necessary change this time. Read: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and BookmarkingYes you are right Do you have an idea to answer my question?
You probably don't have the executable/binary in your PATH. What platform (OS) are you on?
ubuntu19
And how did you install homer? Using
apt-get/a similar package manager or from source?apt-get
That's odd -
apt-getinstall should take care of PATH settings. Did the package install successfully? Can you give us the command you used? Maybe run it again and give us all the output (STDOUT & STDERR) you see.Now I was able to solve the above problem with your guidance. I did not add the executable path correctly.
Thank you very much.