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FIMO vs AME - true positive and false positives across search tools
meme ame fimo motif
updated 5.6 years ago by 20 • written 5.7 years ago by ▴ 420
13
votes
30
replies
8.5k
views
10 follow
BagFoot TF foot printing
R bagfoot bagfootr ChIP-Seq
updated 5.6 years ago by ▴ 20 • written 6.5 years ago by ▴ 420
3
votes
5
replies
1.6k
views
FIMO output that preserves padj values
ChIP-Seq motifs FIMO MEME DESeq2
5.7 years ago by rbronste ▴ 420
0
votes
0
replies
1.4k
views
bwtool stalled liftover
bwtool bigwig liftover
5.7 years ago by rbronste ▴ 420
5
votes
6
replies
2.5k
views
Common gene names list to BED with +/- TSS intervals
RNA-Seq
updated 5.7 years ago by 35k • written 5.7 years ago by ▴ 420
0
votes
1
reply
1.3k
views
RSAT gives strange motif calls
RSAT motif ChIP-Seq
updated 5.9 years ago by ▴ 10 • written 6.2 years ago by ▴ 420
1
vote
4
replies
3.1k
views
bwtool matrix error - invalid signed integer
bwtool matrix software error
updated 5.9 years ago by 20 • written 7.3 years ago by ▴ 420
2
votes
5
replies
2.7k
views
Motif database of choice
motif RSAT ChIP-Seq
updated 6.0 years ago by • 0 • written 6.7 years ago by ▴ 420
2
votes
2
replies
2.1k
views
FIMO target coordinates in fasta file
fimo meme motif fasta
updated 6.0 years ago by 82k • written 6.3 years ago by ▴ 420
1
vote
2
replies
1.2k
views
Fimo output for classes of TFs from specific database
ChIP-Seq fimo meme
updated 6.0 years ago by 35k • written 6.0 years ago by ▴ 420
6
votes
11
replies
3.0k
views
blastn errors following building of database
blast blastn makeblastdb
updated 6.0 years ago by 20 • written 6.0 years ago by ▴ 420
3
votes
3
replies
2.2k
views
Extracting the exact motif location from FIMO
meme fimo motif ChIP-Seq
updated 6.1 years ago by 35k • written 6.1 years ago by ▴ 420
4
votes
8
replies
5.0k
views
samtools faidx error
samtools faidx
updated 6.1 years ago by ▴ 10 • written 6.8 years ago by ▴ 420
1
vote
3
replies
1.0k
views
Adjusting for uneven Nextseq loading
NextSeq fastq sequencing ChIP-Seq
updated 6.1 years ago by 6.4k • written 6.1 years ago by ▴ 420
1
vote
3
replies
1.0k
views
Excluding intervals with repeats
repeats BED masking
6.1 years ago by rbronste ▴ 420
0
votes
2
replies
960
views
Filter HT-Seq output for gene subclasses
htseq RNA-Seq transcription factor
6.3 years ago by rbronste ▴ 420
4
votes
3
replies
1.6k
views
Extracting interval from fasta header
fasta header bed interval
updated 6.3 years ago by 35k • written 6.3 years ago by ▴ 420
3
votes
6
replies
3.1k
views
FIMO output to bed
fimo meme bedops bedtools
updated 6.3 years ago by ★ 1.7k • written 6.3 years ago by ▴ 420
1
vote
4
replies
1.3k
views
Splitting .bed file by genomic location
ChIP-Seq R BED promoter
6.3 years ago by rbronste ▴ 420
0
votes
1
reply
1.3k
views
FIMO outputs only Chr1 hits
fimo meme motif
updated 6.4 years ago by ★ 1.6k • written 6.4 years ago by ▴ 420
0
votes
1
reply
1.6k
views
De-novo motif discovery and repeats
motif meme fimo de novo
updated 6.4 years ago by 35k • written 6.4 years ago by ▴ 420
3
votes
5
replies
3.2k
views
Subsetting DESeq2 results by padj quantity
DESeq2 DESeq R
updated 6.4 years ago by ▴ 690 • written 6.4 years ago by ▴ 420
0
votes
2
replies
2.5k
views
HOMER target sequence location
HOMER ChIP-Seq motif
updated 6.4 years ago by ▴ 30 • written 7.2 years ago by ▴ 420
2
votes
5
replies
1.5k
views
Displaying/plotting numerous biological comparisons
plotting R
updated 6.5 years ago by 20 • written 6.6 years ago by ▴ 420
1
vote
3
replies
3.1k
views
tagAlign to BAM
ENCODE tagAlign bam
updated 6.5 years ago by 7.1k • written 6.5 years ago by ▴ 420
4
votes
9
replies
2.6k
views
Bed to BAM information transfer
ChIP-Seq sequencing BAM bed footprinting
updated 6.5 years ago by 20 • written 7.2 years ago by ▴ 420
2
votes
11
replies
1.7k
views
Converting raw counts or DEseq2 output to TxDb container
RNA-Seq R gene
updated 6.6 years ago by ▴ 360 • written 6.6 years ago by ▴ 420
2
votes
3
replies
2.9k
views
ChIPseeker missing full annotation
ChIPSeeker ChIP-Seq KEGG GO
updated 6.6 years ago by ▴ 360 • written 6.6 years ago by ▴ 420
2
votes
3
replies
1.5k
views
Eliminating repetetive motifs found by MEME
MEME motif ChIP-Seq
updated 6.6 years ago by 35k • written 6.6 years ago by ▴ 420
0
votes
1
reply
1.6k
views
MEME motif width
ChIP-Seq meme motif
6.6 years ago by rbronste ▴ 420
1
vote
1
reply
1.8k
views
Masking repeats in ATAC-seq data
ATAC-seq repeats DESeq
6.7 years ago by rbronste ▴ 420
0
votes
4
replies
1.8k
views
EP300 ChIP-seq in the brain
ChIP-Seq
updated 6.7 years ago by ▴ 10 • written 7.0 years ago by ▴ 420
1
vote
3
replies
2.6k
views
Comparing open chromatin data to ChromHMM model
chromHMM ChIP-Seq ATAC-seq
updated 6.8 years ago by 20 • written 6.9 years ago by ▴ 420
4
votes
5
replies
2.0k
views
Normalizing Illumina fastq read-lengths from different GEO datasets
GEO fastq RNA-Seq
6.8 years ago by rbronste ▴ 420
0
votes
5
replies
1.9k
views
Galaxy Bowtie2 fastq recognition
galaxy Bowtie2 fastq
6.8 years ago by rbronste ▴ 420
23
votes
9
replies
8.8k
views
Removing PCR duplicates - fastq or BAM?
alignment BAM fastq duplicates
updated 6.8 years ago by 100k • written 6.8 years ago by ▴ 420
1
vote
3
replies
3.3k
views
Samtools flagstat unpaired reads
samtools BAM Bowtie2
updated 6.8 years ago by 161k • written 6.8 years ago by ▴ 420
2
votes
2
replies
4.6k
views
Duplicates in ATAC-seq data
ATAC-seq picard samtools rmdup duplicates
updated 6.8 years ago by ★ 3.4k • written 6.8 years ago by ▴ 420
0
votes
2
replies
2.1k
views
Bowtie2 parallelization on cluster
Bowtie2 alignment
updated 6.8 years ago by ▴ 110 • written 6.8 years ago by ▴ 420
0
votes
1
reply
17k
views
Trouble installing R package Cairo
R Cairo
updated 6.9 years ago by ▴ 330 • written 6.9 years ago by ▴ 420
4
votes
21
replies
3.0k
views
Closest gene to set of intervals
bedops bedtools
updated 6.9 years ago by ★ 1.5k • written 6.9 years ago by ▴ 420
4
votes
1
reply
2.1k
views
deepTools - plotHeatmap, move colorbar to the bottom
deepTools heatmap
updated 6.9 years ago by 104k • written 6.9 years ago by ▴ 420
0
votes
3
replies
1.2k
views
Table Browser refGene identifiers question
Table Browser UCSC
updated 6.9 years ago by 161k • written 6.9 years ago by ▴ 420
4
votes
4
replies
1.6k
views
Chromatin Accessibility Data and RNA-seq
RNA-Seq chromatin accessibility
updated 6.9 years ago by 13k • written 6.9 years ago by ▴ 420
1
vote
2
replies
1.2k
views
Peak ident near highly expressed genes
ChIP-Seq RNA-Seq bedops
6.9 years ago by rbronste ▴ 420
0
votes
0
replies
1.3k
views
Normalizing CENTIPEDE footprint plots
centipede ATAC-seq footprinting ChIP-Seq R
updated 7.0 years ago by 20 • written 7.1 years ago by ▴ 420
2
votes
8
replies
3.2k
views
Getting avg gene length from GTF (for all splice isoforms)
RNA-Seq UCSC table browser GTF
updated 7.0 years ago by 35k • written 7.0 years ago by ▴ 420
10
votes
6
replies
1.8k
views
Setting up a lab wiki
wiki data analysis and organization
updated 7.0 years ago by 27k • written 7.0 years ago by ▴ 420
2
votes
9
replies
2.8k
views
Calculating FPKM values from HT-counts
FPKM RPKM RNA-Seq
updated 7.0 years ago by 104k • written 7.0 years ago by ▴ 420
0
votes
5
replies
2.6k
views
bedops wig2bed issue
bedops wig2bed
7.0 years ago by rbronste ▴ 420
119 results • Page 2 of 3
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