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Forum: Variant calling (SNV/InDel): is only using properly paired reads recommended?
mapping variants
updated 4 weeks ago by 149k • written 4 weeks ago by 6.1k
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676
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Comment: Comment: Why counting by diffbind and featurecounts differ?
4 months ago by Ian 6.1k
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0
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859
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Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
4 months ago by Ian 6.1k
1
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1
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859
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Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
4 months ago by Ian 6.1k
7
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8
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859
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Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, and intron only
rna-seq featurecounts
4 months ago by Ian 6.1k
1
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0
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859
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Answer: Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
4 months ago by Ian 6.1k
1
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1
reply
859
views
Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
4 months ago by Ian 6.1k
0
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0
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859
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Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
4 months ago by Ian 6.1k
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0
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5.7k
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Comment: Comment: How to use output from GeneMark-ES to identify function?
4 months ago by Ian 6.1k
1
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0
replies
901
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Comment: Comment: Trying to understand basic DiffBind usage
5 months ago by Ian 6.1k
1
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1
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901
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Answer: Answer: Trying to understand basic DiffBind usage
5 months ago by Ian 6.1k
0
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0
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822
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Comment: Comment: Confirmation required on how DiffBind generates union of regions (min. 1bp overl
6 months ago by Ian 6.1k
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1
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822
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Comment: Comment: Confirmation required on how DiffBind generates union of regions (min. 1bp overl
7 months ago by Ian 6.1k
0
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4
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822
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Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
4 months ago by Ian 6.1k
0
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1
reply
975
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Comment: Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
9 months ago by Ian 6.1k
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0
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751
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Answer: Answer: How to make the Input track flat for ChIP-seq
13 months ago by Ian 6.1k
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0
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961
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Answer: Answer: DEG gene list and find common TF from public ChlP-Seq data
16 months ago by Ian 6.1k
13
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6
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4.2k
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Are there mm39/GRCm39 blacklist regions?
blacklist
updated 18 months ago by 13k • written 2.8 years ago by 6.1k
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1
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1.2k
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How to convert a HG19 Hi-C hic file to HG38?
Hi-C hic
updated 20 months ago by • 0 • written 3.6 years ago by 6.1k
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0
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1.5k
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Comment: Comment: Custom genome installation in SigProfileMatrixGenerator
22 months ago by Ian 6.1k
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1
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1.1k
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Answer: Answer: macs2 for centromere chip-seq peak calling
23 months ago by Ian 6.1k
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0
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1.5k
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Comment: Comment: ChIP-seq problem
2.2 years ago by Ian 6.1k
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1
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1.5k
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Comment: Comment: ChIP-seq problem
2.2 years ago by Ian 6.1k
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1
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1.4k
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Answer: Answer: How to create bigwig file in galaxy after MACS procedure(Chip Seq)
2.2 years ago by Ian 6.1k
1
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1
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1.6k
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Answer: Answer: Upregulated and downregulated genes from ChIP-seq data
2.2 years ago by Ian 6.1k
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0
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4.2k
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Comment: Comment: Are there mm39/GRCm39 blacklist regions?
2.8 years ago by Ian 6.1k
0
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0
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4.2k
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Comment: Comment: Are there mm39/GRCm39 blacklist regions?
2.8 years ago by Ian 6.1k
0
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1
reply
1.7k
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Comment: Comment: How to count mapping rates for ChIP-seq?
2.8 years ago by Ian 6.1k
3
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2
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5.7k
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Answer: Answer: How to use output from GeneMark-ES to identify function?
3.3 years ago by Ian 6.1k
1
vote
3
replies
1.5k
views
Custom genome installation in SigProfileMatrixGenerator
genome custom SigProfilerMatrixGenerator
22 months ago by Ian 6.1k
1
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1
reply
1.5k
views
Answer: Answer: Custom genome installation in SigProfileMatrixGenerator
3.7 years ago by Ian 6.1k
1
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3
replies
1.4k
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Tool/method to calculate the sequence context of variants?
sequence context variant
3.8 years ago by Ian 6.1k
1
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0
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1.4k
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Answer: Answer: Tool/method to calculate the sequence context of variants?
3.8 years ago by Ian 6.1k
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0
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1.4k
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Comment: Comment: Tool/method to calculate the sequence context of variants?
3.8 years ago by Ian 6.1k
3
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3
replies
2.7k
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Comparing input read subtracted ChIP-read profiles using Deeptools v3.4.3
deeptools
4.4 years ago by Ian 6.1k
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1
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2.7k
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Comment: C: Comparing input read subtracted ChIP-read profiles using Deeptools2
4.4 years ago by Ian 6.1k
8
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2
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6.7k
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Bedtools Intersectbed
bedtools intersect coverage coverage
updated 4.4 years ago by 20 • written 13.3 years ago by 6.1k
7
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0
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71k
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
updated 4.7 years ago by 44k • written 13.8 years ago by 6.1k
1
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0
replies
71k
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Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics?
updated 4.7 years ago by 44k • written 13.8 years ago by 6.1k
3
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1
reply
7.8k
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Tool: Weeder 2.0 - motif discovery tool updated
motif-discovery chip-seq weeder
updated 20 months ago by 44k • written 10.3 years ago by 6.1k
6
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0
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5.1k
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Answer: A: MACS2 Peak Calling : Different number of peaks for each replicate
updated 5.1 years ago by 44k • written 9.1 years ago by 6.1k
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0
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5.3k
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Answer: A: DiffBind - DESeq2 Consensus peakset
updated 5.1 years ago by 44k • written 10.8 years ago by 6.1k
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0
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5.3k
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Answer: A: how to calculate distance between CpG site and TSS?
updated 5.1 years ago by 44k • written 10.8 years ago by 6.1k
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1
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26k
views
Comment: C: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
updated 5.2 years ago by 44k • written 10.8 years ago by 6.1k
1
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0
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9.9k
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Answer: A: Read depth and Hi-C resolution
updated 5.2 years ago by 44k • written 9.1 years ago by 6.1k
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1
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12k
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Answer: A: Difference between UCSC and Ensembl genomes
updated 5.2 years ago by 44k • written 9.1 years ago by 6.1k
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0
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26k
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Comment: C: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
updated 5.2 years ago by 44k • written 10.8 years ago by 6.1k
2
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1
reply
1.4k
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Answer: A: found non conserved regions between 2 genomes
5.2 years ago by Ian 6.1k
2
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0
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3.4k
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Answer: A: Program For Filtering Solid Reads
updated 5.2 years ago by 44k • written 11.8 years ago by 6.1k
0
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1
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22k
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Answer: A: Error when trying to use samtools to convert a sam files to a bam file
updated 5.2 years ago by 44k • written 9.2 years ago by 6.1k
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