FIMO keep all results

As i understand in FIMO "The maximum number of stored matches is 100,000" by default. Using --max-stored-scores can increase the number of stored scores but what if i want to keep all the results? Is there an option for that?

fimo

• 737 views • link

updated 2.4 years ago by Mensur Dlakic

• written 2.4 years ago by mathalfilip •

1 answer

If you set the --max-stored-scores switch to a crazy high number, say --max-stored-scores 100000000, it is a safe bet that all the results will be saved.

• 0 views • link

written 2.4 years ago by Mensur Dlakic

More posts like this

Motif Scanning: HOMER vs MEME, settings?
written 2.4 years ago by mb •

Hello, I need to do a motif density plot of the whole genome, as we have a subset of 400 genes where we expect a …
Doublechecking enrichment of promoters of DE genes
written 2.6 years ago by Aspire

I have performed an enrichment analysis over the promoters of genes that are differentially expressed between two conditions, and there were highly significant results. However, …
Is there a similar option to Diamond's --max-target-seqs in MMSeqs2?
written 4.4 years ago by O.rka

Is there an option for the maximum number of target seqs (similar to --max-target-seqs in Diamond)? I found this: --max-seqs INT Maximum results per query …
FIMO --max-stored-scores option
written 5.4 years ago by lessismore

Dear all, according to FIMO guidelines the option `--max-stored-scores` > Set the maximum number of scores that will be stored. Keeping a > complete list …
circos error - no change to housekeeping.conf
written 5.6 years ago by Obex33 •

Hi, I want to plot a histogram of my mapped reads to Virus genome. I keep getting the error "but the maximum is currently set …
Tutorial: Finding individual motif occurrences with FIMO from the MEME suite
written 7.7 years ago by ATpoint

A common task, frequently asked here on Biostars, is to find out if a given DNA sequence contains certain motifs. This can be done with …
MEME result v FIMO result for target annotation
written 8.6 years ago by BioinfGuru

Hi all, For simplicity I have a single sample that I have run meme-chip on. Also, for simplicity lets assume there is a single motif …
Can we use MeMe motif output result and prepare tree from motif
written 9.1 years ago by Vinay Singh •

hello all, I am using MeMe motif analysis server for my protein sequences analysis, in result i am getting html file with block diagram of …
meme text format
written 12.2 years ago by Assa Yeroslaviz

Hi I am trying to run fimo from the meme suite but can't make my sequence file readable. I keep getting the error > fimo …
Bwa Gapped Alignment
written 14.4 years ago by Bioscientist

<p>bwa aln has the option "-o INT Maximum number of gap opens [1] " Does this mean by default maximum only 1 gap is allowed? …