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MEME Suite Q&A
1–30 of 665
Welcome to the MEME Suite question and answer forum.
The latest version of the MEME Suite can be used online at
http://meme-suite.org/.
You might get a more immediate response by sending an email to the support address
meme-suite@uw.edu
as more people from the team check that address and some of them even work on weekends...
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aishwarya kulkarni
,
cegrant
2
6/2/20
Q&A
Can't locate HtmlMonolithWr.pm
I responded to your other posting.
unread,
Install
MEME
TOMTOM
Q&A
Can't locate HtmlMonolithWr.pm
I responded to your other posting.
6/2/20
Laura Pineda
,
cegrant
4
5/28/20
Q&A
MEME's motifs have an E-vaue too high
I'd suggest a few things. First, since you are looking for a known promoter you might consider
unread,
MEME
Meme-Suite
motif_discovery
Q&A
MEME's motifs have an E-vaue too high
I'd suggest a few things. First, since you are looking for a known promoter you might consider
5/28/20
Trevor C
,
cegrant
2
5/12/20
Q&A
-evt argument in meme not working.
The problem is that MEME is a greedy algorithm and is not guaranteed to identify motifs in strictly
unread,
MEME
Meme-Suite
Q&A
-evt argument in meme not working.
The problem is that MEME is a greedy algorithm and is not guaranteed to identify motifs in strictly
5/12/20
Skyler
, …
Joel Wallenius
6
3/19/20
Q&A
meme -p incompatible with (my) bash while loops?
Thank you Joel. That is more precise/concise and it solves the problem. Expert or no, I appreciate
unread,
MEME
MEME-ChIP
motif_discovery
Q&A
meme -p incompatible with (my) bash while loops?
Thank you Joel. That is more precise/concise and it solves the problem. Expert or no, I appreciate
3/19/20
Yusuke Takahashi
3/12/20
[Enhancement] The default value of maxsites of meme is confusing
Dear All, Under some conditions, "maxsites" is cut off at 1000. This behavior, I think, is
unread,
MEME
[Enhancement] The default value of maxsites of meme is confusing
Dear All, Under some conditions, "maxsites" is cut off at 1000. This behavior, I think, is
3/12/20
Yusuke Takahashi
,
cegrant
4
3/28/20
Q&A
meme may return floating number maxsites, which causes an error in meme_xml_to_html
Hi Yusuke, I'm not familiar with the protocols for working with DNA modification loci, and so I
unread,
MEME
MEME-ChIP
Q&A
meme may return floating number maxsites, which causes an error in meme_xml_to_html
Hi Yusuke, I'm not familiar with the protocols for working with DNA modification loci, and so I
3/28/20
Pushya Krishna
,
cegrant
2
8/20/19
Q&A
Entire test either skipped or failed?
how can I get meme2meme and the other motif format utilities to work? Users had pointed out to us
unread,
Install
MEME
Meme-Suite
Q&A
Entire test either skipped or failed?
how can I get meme2meme and the other motif format utilities to work? Users had pointed out to us
8/20/19
Kashif Nawaz
,
CharlesEGrant
2
3/13/19
Q&A
Convert Fasta format to MEME-motif format
Assuming you have the MEME suite installed on your computer, you have access to the scripts here:
unread,
FIMO
MEME
Meme-Suite
Q&A
Convert Fasta format to MEME-motif format
Assuming you have the MEME suite installed on your computer, you have access to the scripts here:
3/13/19
Rdmb
,
cegrant
2
2/13/19
Q&A
AME perl python output issue
By using AME with the following command, the output is similar to the online version but I do not
unread,
AME
MEME
Q&A
AME perl python output issue
By using AME with the following command, the output is similar to the online version but I do not
2/13/19
Lucy
,
cegrant
2
11/27/18
Q&A
How to create priors from ATAC-seq data for FIMO
The documentation for the create-priors script can be found here: http://meme-suite.org/doc/create-
unread,
FIMO
MEME
Q&A
How to create priors from ATAC-seq data for FIMO
The documentation for the create-priors script can be found here: http://meme-suite.org/doc/create-
11/27/18
Ashwini Jeggari
,
CharlesEGrant
2
10/22/18
Q&A
uniprobe pwm to meme format
I tried to run the script using single file. perl uniprobe2meme.pl.in uniprobe_Peterson2012_PWM/Gli1/
unread,
CentriMo
MEME
TOMTOM
motif_discovery
Q&A
uniprobe pwm to meme format
I tried to run the script using single file. perl uniprobe2meme.pl.in uniprobe_Peterson2012_PWM/Gli1/
10/22/18
Nick Riddiford
,
CharlesEGrant
3
7/24/18
Q&A
Enrichment of de-novo discovered motifs
Hi Charles, Thanks a lot for your very helpful and detailed response. We are looking for motifs
unread,
AME
MEME
Q&A
Enrichment of de-novo discovered motifs
Hi Charles, Thanks a lot for your very helpful and detailed response. We are looking for motifs
7/24/18
jiecon...@gmail.com
,
CharlesEGrant
2
7/10/18
Q&A
/bin/bash: compile: command not found when using MAKE
The "compile not found" message ndicates that you don't have the Java build tool, ant,
unread,
MEME
Q&A
/bin/bash: compile: command not found when using MAKE
The "compile not found" message ndicates that you don't have the Java build tool, ant,
7/10/18
jiecon...@gmail.com
,
CharlesEGrant
2
7/5/18
Q&A
Question about update-sequence-db --ucsc
Thanks for letting us know about the problem. We're always in a race to keep up with changes to
unread,
MEME
Q&A
Question about update-sequence-db --ucsc
Thanks for letting us know about the problem. We're always in a race to keep up with changes to
7/5/18
Sarah Lerch
, …
CharlesEGrant
3
4/17/18
Q&A
MEME errors: 'psp_sum > 0' failed and (core dumped)
Could you attach or forward us a copy of the input sequences? That would help us troubleshoot the
unread,
MEME
Q&A
MEME errors: 'psp_sum > 0' failed and (core dumped)
Could you attach or forward us a copy of the input sequences? That would help us troubleshoot the
4/17/18
Robert Leach
,
cegrant
2
3/7/18
Q&A
Why is this command stopping after finding 1 motif?
You need to specify the number of motifs you want MEME to find, using the '-nmotifs' option.
unread,
MEME
motif_discovery
Q&A
Why is this command stopping after finding 1 motif?
You need to specify the number of motifs you want MEME to find, using the '-nmotifs' option.
3/7/18
mdok...@fiu.edu
,
CharlesEGrant
2
2/12/18
Q&A
MEME-ChIP results interpretation
It looks like the masking of short repeats was incomplete. You don't mention what tool you used
unread,
MEME
MEME-ChIP
motif_discovery
Q&A
MEME-ChIP results interpretation
It looks like the masking of short repeats was incomplete. You don't mention what tool you used
2/12/18
Joel Wallenius
,
CharlesEGrant
3
1/19/18
Q&A
nsites lower than the number of sequences despite using OOPS
I would but I already removed all output and re-ran everything. I can't replicate the issue, it
unread,
MEME
motif_discovery
Q&A
nsites lower than the number of sequences despite using OOPS
I would but I already removed all output and re-ran everything. I can't replicate the issue, it
1/19/18
Joel Wallenius
,
CharlesEGrant
4
1/18/18
Q&A
Is there a way to tell MEME to search for motifs that are similar to a specific (supplied on input) sequence?
Will it make MEME blind to motifs that are not similar to this consensus sequence? Blind is too
unread,
MEME
Meme-Suite
motif_discovery
Q&A
Is there a way to tell MEME to search for motifs that are similar to a specific (supplied on input) sequence?
Will it make MEME blind to motifs that are not similar to this consensus sequence? Blind is too
1/18/18
Joel Wallenius
,
CharlesEGrant
5
1/8/18
Q&A
MEME stops without errors after finding the first motif
You can treat the E-value a p-value controlled for the size of the input sequence data. The
unread,
MEME
motif_discovery
Q&A
MEME stops without errors after finding the first motif
You can treat the E-value a p-value controlled for the size of the input sequence data. The
1/8/18
Joel Wallenius
,
CharlesEGrant
5
12/27/17
Q&A
The minsites option does not work?
Thank you Charles!
unread,
MEME
motif_discovery
Q&A
The minsites option does not work?
Thank you Charles!
12/27/17
Alex Reynolds
,
CharlesEGrant
3
6/14/17
Q&A
Required system property X509_USER_PROXY not set
First, version 4.11.0 is a bit old. The current version of the MEME Suite is 4.11.4. This is probably
unread,
Build
Install
MEME
Q&A
Required system property X509_USER_PROXY not set
First, version 4.11.0 is a bit old. The current version of the MEME Suite is 4.11.4. This is probably
6/14/17
Hiko Wong
,
CharlesEGrant
2
5/16/17
Q&A
MEME suite install error
If you look in the file tests/scripts/dreme.log you should find detailed information about why the
unread,
MEME
Meme-Suite
Q&A
MEME suite install error
If you look in the file tests/scripts/dreme.log you should find detailed information about why the
5/16/17
gatla
,
CharlesEGrant
3
5/16/17
Q&A
MEME de-novo motif discovery - parameters
1. I am centering the peaks of my interest and trying to call denovo motifs with different flanking
unread,
MEME
fasta-get-markov
motif_discovery
Q&A
MEME de-novo motif discovery - parameters
1. I am centering the peaks of my interest and trying to call denovo motifs with different flanking
5/16/17
Varsha Sundaresan
,
CharlesEGrant
5
2/21/17
Q&A
meme mast overlapping motif search
HI Charles, I will try out FIMO. Thank you so much!
unread,
MAST
MEME
Q&A
meme mast overlapping motif search
HI Charles, I will try out FIMO. Thank you so much!
2/21/17
Santhilal Subhash
,
CharlesEGrant
2
2/20/17
Q&A
Installation Error (CRASH)
In the linked log all of the failures are associated with this error message: /usr/bin/perl: symbol
unread,
MEME
MEME-ChIP
TOMTOM
Q&A
Installation Error (CRASH)
In the linked log all of the failures are associated with this error message: /usr/bin/perl: symbol
2/20/17
Arun Prasanna
,
CharlesEGrant
2
2/11/17
Q&A
ceqlogo error "No motifs were specified"
Here is the documentation for the ceqlogo command: http://meme-suite.org/doc/ceqlogo.html You have to
unread,
Logograms
MEME
motif_discovery
Q&A
ceqlogo error "No motifs were specified"
Here is the documentation for the ceqlogo command: http://meme-suite.org/doc/ceqlogo.html You have to
2/11/17
Arun Prasanna
,
CharlesEGrant
2
1/16/17
Q&A
Unable to get a statistically significant motif
The traditional threshold for a significant p-value or value is 0.01 or 0.05. While this is only a
unread,
MEME
Meme-Suite
motif_discovery
Q&A
Unable to get a statistically significant motif
The traditional threshold for a significant p-value or value is 0.01 or 0.05. While this is only a
1/16/17
Varsha Sundaresan
,
CharlesEGrant
3
1/12/17
Q&A
How to get mast meme output as bed format file
I just found out the command to get the bed format was use -hit_list in the command line option with
unread,
MAST
MEME
Q&A
How to get mast meme output as bed format file
I just found out the command to get the bed format was use -hit_list in the command line option with
1/12/17
Arun Prasanna
,
CharlesEGrant
2
1/5/17
Q&A
Query on MEME sites
MEME is also a greedy algorithm, so as soon as it has enough information to estimate the statistical
unread,
MEME
motif_discovery
Q&A
Query on MEME sites
MEME is also a greedy algorithm, so as soon as it has enough information to estimate the statistical
1/5/17