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Comment: Comment: remove unmapped reads on a specific chromosome only
2.5 years ago by firatuyulur ▴ 320
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Comment: Comment: remove unmapped reads on a specific chromosome only
2.5 years ago by firatuyulur ▴ 320
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1.5k
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remove unmapped reads on a specific chromosome only
bam remove unmapped
updated 2.5 years ago by 17k • written 2.5 years ago by ▴ 320
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Comment: C: Bam File: Change Chromosome Notation
2.6 years ago by firatuyulur ▴ 320
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848
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Comment: C: genome in IGV session file
3.2 years ago by firatuyulur ▴ 320
2
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2
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2.2k
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finding unique mutations from a multi-sample VCF
SNP vcf
updated 3.4 years ago by 20 • written 6.5 years ago by ▴ 320
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734
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Comment: C: str handling in python
3.9 years ago by firatuyulur ▴ 320
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4.0k
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Answer: A: I need allele copy number information for running PyClone
4.0 years ago by firatuyulur ▴ 320
2
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1
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1.6k
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Answer: A: equal distance between groups in a barplot
5.2 years ago by firatuyulur ▴ 320
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1
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3.6k
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Comment: C: removing outliers before running DESeq2
5.2 years ago by firatuyulur ▴ 320
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1.1k
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Comment: C: size of the pathways for analysis and filtration
5.2 years ago by firatuyulur ▴ 320
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3
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1.1k
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size of the pathways for analysis and filtration
pathways RNA-Seq enrichment
5.2 years ago by firatuyulur ▴ 320
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1
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7.8k
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Answer: A: rRNA remove from RNAseq data
5.2 years ago by firatuyulur ▴ 320
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0
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1.1k
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Normalizing count data with several treatment dosages
RNA-Seq normalization deseq2 edgeR QC
5.5 years ago by firatuyulur ▴ 320
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1
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1.1k
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comparing DEGs with same treatment but different control batch
deseq2 RNA-Seq statistics correlation
updated 5.6 years ago by 13k • written 5.6 years ago by ▴ 320
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2.0k
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Comment: C: plotting an expression data in heat map/ hierarchical clustering
5.6 years ago by firatuyulur ▴ 320
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1
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7.4k
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Answer: A: ATAC-seq: differential peaks using macs2 bdgdiff yields strange results
5.6 years ago by firatuyulur ▴ 320
9
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3
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3.2k
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enhancer RNA counting from RNASeq data
RNA-Seq enhancer RNA read counts
updated 5.6 years ago by ▴ 30 • written 6.8 years ago by ▴ 320
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1
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8.1k
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Answer: A: Filter by Fold change in DESeq2
6.1 years ago by firatuyulur ▴ 320
1
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1
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2.3k
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Comment: C: Optimization of RNA-Seq data mapping with tophat2
6.1 years ago by firatuyulur ▴ 320
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2.4k
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Answer: A: From bam files to isoform read counts
6.1 years ago by firatuyulur ▴ 320
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4.2k
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Comment: C: macs2 normalization on broadPeak
6.2 years ago by firatuyulur ▴ 320
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4.2k
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Comment: C: macs2 normalization on broadPeak
6.2 years ago by firatuyulur ▴ 320
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1
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4.2k
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Comment: C: macs2 normalization on broadPeak
6.2 years ago by firatuyulur ▴ 320
4
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5
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4.2k
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macs2 normalization on broadPeak
callpeak atac-seq macs2
updated 3 months ago by 40k • written 6.2 years ago by ▴ 320
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0
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2.0k
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Comment: C: Zero expression in cuffdiff
6.2 years ago by firatuyulur ▴ 320
1
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1
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1.5k
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rnaseq data vs. phenotype
RNA-Seq deseq2 tophat2
6.2 years ago by firatuyulur ▴ 320
1
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3
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2.6k
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Comment: C: LASTZ does not accept/like "-" (dash) in Fasta file
6.3 years ago by firatuyulur ▴ 320
1
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1
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7.9k
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Answer: A: Threshold of removing genes with low counts ?
6.4 years ago by firatuyulur ▴ 320
1
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1
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2.5k
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Comment: C: Widening the distances between PCA vectors in PCA a biplot
6.4 years ago by firatuyulur ▴ 320
2
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3.8k
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Answer: A: I am a student, what can i do with 23andme raw data?
6.5 years ago by firatuyulur ▴ 320
5
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1
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2.8k
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Plus and minus strands plotted together
GRO-Seq ChIP-Seq Figure
6.6 years ago by firatuyulur ▴ 320
4
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0
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2.8k
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Answer: A: Plus and minus strands plotted together
6.6 years ago by firatuyulur ▴ 320
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1
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1.9k
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Comment: C: multiple SRR in a particular FTP conflict
6.6 years ago by firatuyulur ▴ 320
0
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4
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1.9k
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multiple SRR in a particular FTP conflict
ChIP-Seq
updated 6.6 years ago by 7.5k • written 6.6 years ago by ▴ 320
1
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0
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2.3k
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rMATS readlength difference
rMATS RNA-Seq Splicing
6.6 years ago by firatuyulur ▴ 320
1
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1
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2.3k
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Comment: C: RNA-Seq analysis with standard p-value
6.7 years ago by firatuyulur ▴ 320
1
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0
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1.6k
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Comment: C: Cuffdiff output filtering based on significance
6.7 years ago by firatuyulur ▴ 320
1
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1
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1.6k
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Answer: A: Cuffdiff output filtering based on significance
6.7 years ago by firatuyulur ▴ 320
5
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3
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1.7k
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Methylation levels at specific sites
ChIP-Seq BED Wiggle
updated 6.7 years ago by 35k • written 6.7 years ago by ▴ 320
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1.7k
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Comment: C: Methylation levels at specific sites
6.7 years ago by firatuyulur ▴ 320
0
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1.5k
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Answer: A: differential expression analysis
6.7 years ago by firatuyulur ▴ 320
1
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0
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3.1k
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Answer: A: How can I count one specific exon in RNA-seq data
6.7 years ago by firatuyulur ▴ 320
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1
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3.2k
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Comment: C: replicates in edgeR and DESeq2
6.7 years ago by firatuyulur ▴ 320
3
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1
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1.9k
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Comment: C: Is It Fastq Format
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 320
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1.9k
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Comment: C: Is It Fastq Format
6.7 years ago by firatuyulur ▴ 320
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2.5k
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Comment: C: differential gene expression analysis
6.7 years ago by firatuyulur ▴ 320
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0
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1.9k
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Answer: A: Is It Fastq Format
6.7 years ago by firatuyulur ▴ 320
2
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1
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2.6k
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Answer: A: Using Normalized values in Differential Expression Software
6.9 years ago by firatuyulur ▴ 320
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