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Showing :
questions
13
votes
6
replies
2.9k
views
Are there mm39/GRCm39 blacklist regions?
blacklist
updated 8 months ago by
igor
13k • written 23 months ago by
Ian
6.0k
1
vote
1
reply
896
views
How to convert a HG19 Hi-C hic file to HG38?
Hi-C
hic
updated 10 months ago by
Y
• 0 • written 2.8 years ago by
Ian
6.0k
1
vote
3
replies
1.1k
views
Custom genome installation in SigProfileMatrixGenerator
genome
custom
SigProfilerMatrixGenerator
12 months ago by
Ian
6.0k
1
vote
3
replies
1.2k
views
Tool/method to calculate the sequence context of variants?
sequence
context
variant
3.0 years ago by
Ian
6.0k
3
votes
3
replies
2.2k
views
Comparing input read subtracted ChIP-read profiles using Deeptools v3.4.3
deeptools
3.6 years ago by
Ian
6.0k
8
votes
2
replies
6.3k
views
Bedtools Intersectbed
bedtools
intersect
coverage
coverage
updated 3.6 years ago by
Biostar
20 • written 12.5 years ago by
Ian
6.0k
6
votes
3
replies
9.3k
views
Ion Torrent Fastq Format Type?
ion-torrent
fastq
updated 4.6 years ago by
lakhujanivijay
5.8k • written 12.0 years ago by
Ian
6.0k
1
vote
4
replies
1.6k
views
Help need to use information in an multiple fasta alignment (MFA) file?
alignment
fasta
updated 4.7 years ago by
GenoMax
142k • written 4.7 years ago by
Ian
6.0k
10
votes
7
replies
6.0k
views
Conversion Of Bar To Wig Format
chip-seq
wiggle
updated 5.7 years ago by
Ram
43k • written 13.8 years ago by
Ian
6.0k
24
votes
9
replies
17k
views
Extracting Paired-End Reads Sitting In Different Chromosomes
samtools
paired
updated 5.8 years ago by
Stephane Plaisance
▴ 460 • written 12.2 years ago by
Ian
6.0k
5
votes
4
replies
2.4k
views
Method for creating an EMBL formatted annotated sequence?
sequence
ENA
EMBL
6.2 years ago by
Ian
6.0k
0
votes
2
replies
3.5k
views
Extracting Ucsc Canonical Gene Information
ucsc
updated 6.2 years ago by
Biostar
20 • written 12.7 years ago by
Ian
6.0k
5
votes
6
replies
2.6k
views
How to extend variable length intervals to the same final length?
bedtools
slop
intervals
footprint
updated 7.2 years ago by
Alex Reynolds
35k • written 7.2 years ago by
Ian
6.0k
3
votes
5
replies
2.8k
views
Problem viewing a bigWig file on UCSC browser - any debugging solutions?
ucsc
bigwig
8.0 years ago by
Ian
6.0k
7
votes
3
replies
2.5k
views
Differential methylation analysis: sequencing biological replicates versus pooled samples?
dma
differential-methylation
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Ian
6.0k
7
votes
6
replies
3.2k
views
Best to overlap hundreds of BED files to one master BED file?
bed
overlap
intersect
updated 18 months ago by
Ram
43k • written 8.8 years ago by
Ian
6.0k
8
votes
1
reply
3.5k
views
How to add gene annotation to a UCSC assembly hub?
assembly
hub
gtf
gff3
UCSC
updated 23 months ago by
Ram
43k • written 9.1 years ago by
Ian
6.0k
3
votes
5
replies
4.5k
views
htseq-count problem with --samout option
htseq-count
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Ian
6.0k
4
votes
3
replies
8.8k
views
Regular expression matching with Python and biopython SeqIO
regular-expression
python
biopython
updated 3.1 years ago by
Ram
43k • written 9.4 years ago by
Ian
6.0k
13
votes
2
replies
8.0k
views
Should the reads of biological replicates be combined for ChIP-seq peak calling?
ChIP-Seq
replicates
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Ian
6.0k
2
votes
2
replies
8.1k
views
Best way to map paired-end, uniquely mapped reads with Bowtie2?
ChIP-Seq
bowtie
paired-end
updated 2.6 years ago by
Ram
43k • written 10.1 years ago by
Ian
6.0k
18
votes
7
replies
12k
views
How To Plot Read Coverage Over Many Different Genomic Regions?
coverage
chip-seq
updated 10.1 years ago by
Fidel
★ 2.0k • written 11.3 years ago by
Ian
6.0k
17
votes
8
replies
7.4k
views
6 follow
How To Plot/Visualise Tfbs Positions Relative To Tss For Thousands Of Genes?
visualization
transcription
binding
updated 10.1 years ago by
parra.gonzalo
▴ 40 • written 12.1 years ago by
Ian
6.0k
8
votes
5
replies
4.1k
views
How To Combine Solid Ngs Reads From Technical Replicates
solid
replicates
updated 10.2 years ago by
Biostar
20 • written 13.6 years ago by
Ian
6.0k
0
votes
0
replies
3.8k
views
Problem Using Gencode Gene Annotation Gtf With Tophat And Discrepancy Between Ucsc/Gencode Gtfs
tophat
gtf
ucsc
updated 2.2 years ago by
Ram
43k • written 10.2 years ago by
Ian
6.0k
11
votes
9
replies
9.1k
views
6 follow
Ion Torrent Mapping
ion-torrent
mapping
updated 10.2 years ago by
Biostar
20 • written 12.1 years ago by
Ian
6.0k
1
vote
2
replies
2.9k
views
Is It Possible To Manually Reorder Steps In A Galaxy Workflow Summary?
galaxy
workflow
updated 10.3 years ago by
Biostar
20 • written 11.1 years ago by
Ian
6.0k
1
vote
1
reply
4.6k
views
Rsat: How To Interpret Motif 'Sig' Scores In Peak-Motif?
10.7 years ago by
Ian
6.0k
17
votes
4
replies
4.1k
views
Illumina'S New Reduced Resolution Q (Phred) Scores - Good Or Bad?
illumina
updated 10.8 years ago by
Brad Chapman
9.7k • written 10.8 years ago by
Ian
6.0k
5
votes
1
reply
3.4k
views
Can Variants Be Reliably Detected In Duplicated Gene/Region Sequence?
variant-calling
updated 11.1 years ago by
Giovanni M Dall'Olio
28k • written 11.1 years ago by
Ian
6.0k
11
votes
3
replies
5.1k
views
What Are The Best Practices For Faire-Seq Analysis?
updated 11.3 years ago by
Mikael Huss
4.8k • written 11.3 years ago by
Ian
6.0k
4
votes
2
replies
3.3k
views
Suggested Options For Casava 1.8 (Bcl > Fastq)
illumina
fastq
updated 11.9 years ago by
Dan D
7.4k • written 11.9 years ago by
Ian
6.0k
1
vote
1
reply
4.0k
views
Chip-Seq Peak Calling With Ion Torrent Reads
ion-torrent
chip-seq
updated 12.0 years ago by
Ying W
★ 4.2k • written 12.0 years ago by
Ian
6.0k
5
votes
3
replies
3.4k
views
Online Tools To "Prettify" Blast Output
blast
visualization
updated 12.1 years ago by
SES
8.6k • written 12.1 years ago by
Ian
6.0k
4
votes
3
replies
2.7k
views
Chip-Chip Analysis Tools?
chip-seq
updated 12.3 years ago by
Nibua
▴ 70 • written 12.3 years ago by
Ian
6.0k
2
votes
6
replies
3.1k
views
Source Of Drosophila (Dm3) Canonical Transcripts?
ucsc
updated 12.3 years ago by
Mary
11k • written 12.3 years ago by
Ian
6.0k
4
votes
3
replies
7.9k
views
Variant Call Format - Explanation Of Quality Scores?
samtools
vcf
updated 12.9 years ago by
Jeremy Leipzig
22k • written 12.9 years ago by
Ian
6.0k
4
votes
10
replies
14k
views
Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
samtools
vcf
variant
updated 12.9 years ago by
Jeremy Leipzig
22k • written 12.9 years ago by
Ian
6.0k
21
votes
22
replies
12k
views
10 follow
How To Get Non-Overlapping Coordinates From A List That Contains Overlapping Coordinates?
coordinates
overlap
updated 13.0 years ago by
Martin Morgan
★ 1.6k • written 13.0 years ago by
Ian
6.0k
8
votes
5
replies
5.5k
views
Identifying The 'Summit' Coordinate Within Many Coordinates In A Wig File?
wiggle
updated 13.0 years ago by
Pierre Lindenbaum
161k • written 13.0 years ago by
Ian
6.0k
8
votes
10
replies
5.6k
views
6 follow
Interpretation Of Consensus Sequence From Samtools Pileup
samtools
pileup
updated 13.1 years ago by
Pablo Marin-Garcia
★ 2.0k • written 13.1 years ago by
Ian
6.0k
28
votes
26
replies
12k
views
6 follow
How To Efficiently Remove Snps That Are Present In All Samples?
samtools
snp
vcf
updated 13.1 years ago by
Deniz
▴ 210 • written 13.1 years ago by
Ian
6.0k
8
votes
5
replies
4.9k
views
How To Interpret -D File In Samtools Variant Calling Pipeline?
samtools
vcftools
updated 13.1 years ago by
Farhat
★ 2.9k • written 13.1 years ago by
Ian
6.0k
15
votes
4
replies
18k
views
What Is The Difference Between Samtools Mpileup And Pileup
samtools
pileup
mpileup
snp
indel
updated 13.2 years ago by
lh3
33k • written 13.2 years ago by
Ian
6.0k
6
votes
4
replies
2.3k
views
Generating Srf Files From Solid Reads For Archiving - Best Practice?
solid
updated 13.3 years ago by
Jorge Amigo
14k • written 13.3 years ago by
Ian
6.0k
5
votes
1
reply
4.1k
views
Mitochondrial Genome In Chip-Seq?
chip-seq
mitochondria
updated 13.4 years ago by
User 59
13k • written 13.4 years ago by
Ian
6.0k
16
votes
7
replies
5.0k
views
How Best To Add Custom Variation Track To Ucsc Browser?
ucsc
variant
snp
indel
updated 13.6 years ago by
brentp
24k • written 13.6 years ago by
Ian
6.0k
17
votes
14
replies
4.1k
views
How To Split Bar Coded Solid Ngs Reads?
solid
barcode
13.6 years ago by
Ian
6.0k
48 results • Page
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