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Forum: Variant calling (SNV/InDel): is only using properly paired reads recommended?
mapping variants
updated 9 months ago by 154k • written 9 months ago by 6.1k
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1.3k
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Comment: Comment: Why counting by diffbind and featurecounts differ?
13 months ago by Ian 6.1k
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2.0k
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Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
13 months ago by Ian 6.1k
1
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1
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2.0k
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Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
13 months ago by Ian 6.1k
7
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8
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2.0k
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Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, and intron only
rna-seq featurecounts
13 months ago by Ian 6.1k
1
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0
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2.0k
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Answer: Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
13 months ago by Ian 6.1k
1
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1
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2.0k
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Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
13 months ago by Ian 6.1k
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0
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2.0k
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Comment: Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
13 months ago by Ian 6.1k
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0
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6.9k
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Comment: Comment: How to use output from GeneMark-ES to identify function?
13 months ago by Ian 6.1k
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0
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2.4k
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Comment: Comment: Trying to understand basic DiffBind usage
14 months ago by Ian 6.1k
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1
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2.4k
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Answer: Answer: Trying to understand basic DiffBind usage
14 months ago by Ian 6.1k
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1.4k
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Comment: Comment: Confirmation required on how DiffBind generates union of regions (min. 1bp overl
15 months ago by Ian 6.1k
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1
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1.4k
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Comment: Comment: Confirmation required on how DiffBind generates union of regions (min. 1bp overl
16 months ago by Ian 6.1k
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4
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1.4k
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Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
12 months ago by Ian 6.1k
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1
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1.7k
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Comment: Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
18 months ago by Ian 6.1k
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1.2k
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Answer: Answer: How to make the Input track flat for ChIP-seq
22 months ago by Ian 6.1k
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1.5k
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Answer: Answer: DEG gene list and find common TF from public ChlP-Seq data
2.1 years ago by Ian 6.1k
17
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6
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6.3k
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Are there mm39/GRCm39 blacklist regions?
blacklist
updated 2.2 years ago by 13k • written 3.5 years ago by 6.1k
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1
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1.7k
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How to convert a HG19 Hi-C hic file to HG38?
Hi-C hic
updated 2.4 years ago by • 0 • written 4.3 years ago by 6.1k
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0
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2.3k
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Comment: Comment: Custom genome installation in SigProfileMatrixGenerator
2.6 years ago by Ian 6.1k
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1
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1.6k
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Answer: Answer: macs2 for centromere chip-seq peak calling
2.7 years ago by Ian 6.1k
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0
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2.1k
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Comment: Comment: ChIP-seq problem
2.9 years ago by Ian 6.1k
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1
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2.1k
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Comment: Comment: ChIP-seq problem
2.9 years ago by Ian 6.1k
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1
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1.9k
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Answer: Answer: How to create bigwig file in galaxy after MACS procedure(Chip Seq)
2.9 years ago by Ian 6.1k
1
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1
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2.2k
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Answer: Answer: Upregulated and downregulated genes from ChIP-seq data
2.9 years ago by Ian 6.1k
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0
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6.3k
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Comment: Comment: Are there mm39/GRCm39 blacklist regions?
3.5 years ago by Ian 6.1k
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0
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6.3k
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Comment: Comment: Are there mm39/GRCm39 blacklist regions?
3.5 years ago by Ian 6.1k
0
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1
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2.4k
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Comment: Comment: How to count mapping rates for ChIP-seq?
3.5 years ago by Ian 6.1k
3
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2
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6.9k
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Answer: Answer: How to use output from GeneMark-ES to identify function?
4.0 years ago by Ian 6.1k
1
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3
replies
2.3k
views
Custom genome installation in SigProfileMatrixGenerator
genome custom SigProfilerMatrixGenerator
2.6 years ago by Ian 6.1k
1
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1
reply
2.3k
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Answer: Answer: Custom genome installation in SigProfileMatrixGenerator
4.4 years ago by Ian 6.1k
1
vote
3
replies
1.9k
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Tool/method to calculate the sequence context of variants?
sequence context variant
4.5 years ago by Ian 6.1k
1
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0
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1.9k
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Answer: Answer: Tool/method to calculate the sequence context of variants?
4.5 years ago by Ian 6.1k
0
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0
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1.9k
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Comment: Comment: Tool/method to calculate the sequence context of variants?
4.5 years ago by Ian 6.1k
3
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3
replies
3.4k
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Comparing input read subtracted ChIP-read profiles using Deeptools v3.4.3
deeptools
5.1 years ago by Ian 6.1k
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1
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3.4k
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Comment: C: Comparing input read subtracted ChIP-read profiles using Deeptools2
5.1 years ago by Ian 6.1k
8
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2
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7.2k
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Bedtools Intersectbed
bedtools intersect coverage coverage
updated 5.1 years ago by 20 • written 14.0 years ago by 6.1k
7
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0
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116k
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
updated 5.5 years ago by 45k • written 14.6 years ago by 6.1k
1
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0
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116k
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Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics?
updated 5.5 years ago by 45k • written 14.6 years ago by 6.1k
3
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1
reply
8.3k
views
Tool: Weeder 2.0 - motif discovery tool updated
motif-discovery chip-seq weeder
updated 2.4 years ago by 45k • written 11.1 years ago by 6.1k
6
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0
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5.6k
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Answer: A: MACS2 Peak Calling : Different number of peaks for each replicate
updated 5.8 years ago by 45k • written 9.8 years ago by 6.1k
0
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0
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5.7k
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Answer: A: DiffBind - DESeq2 Consensus peakset
updated 5.9 years ago by 45k • written 11.5 years ago by 6.1k
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0
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5.8k
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Answer: A: how to calculate distance between CpG site and TSS?
updated 5.9 years ago by 45k • written 11.5 years ago by 6.1k
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1
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29k
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Comment: C: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
updated 5.9 years ago by 45k • written 11.6 years ago by 6.1k
1
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0
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11k
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Answer: A: Read depth and Hi-C resolution
updated 5.9 years ago by 45k • written 9.8 years ago by 6.1k
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1
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13k
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Answer: A: Difference between UCSC and Ensembl genomes
updated 5.9 years ago by 45k • written 9.8 years ago by 6.1k
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0
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29k
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Comment: C: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
updated 5.9 years ago by 45k • written 11.6 years ago by 6.1k
2
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1
reply
2.0k
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Answer: A: found non conserved regions between 2 genomes
5.9 years ago by Ian 6.1k
2
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0
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3.8k
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Answer: A: Program For Filtering Solid Reads
updated 5.9 years ago by 45k • written 12.5 years ago by 6.1k
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1
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23k
views
Answer: A: Error when trying to use samtools to convert a sam files to a bam file
updated 5.9 years ago by 45k • written 9.9 years ago by 6.1k
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