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4
votes
2
replies
1.4k
views
The number of reads from the BMA file is more than the number of reads from its original FASTQ file
RNA-Seq alignment BAM FASTQ
updated 5.2 years ago by 35k • written 5.2 years ago by ▴ 480
10
votes
10
replies
9.6k
views
6 follow
htseq-count cannot find pysam
htseq-count RNA-Seq quantification HTSeq
updated 3.8 years ago by 45k • written 9.5 years ago by ▴ 480
0
votes
0
replies
3.5k
views
Comment: C: Failed FastQC Per sequence GC content of MeDIP Input sample
updated 5.5 years ago by 45k • written 9.4 years ago by ▴ 480
0
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0
replies
9.6k
views
Comment: C: htseq-count cannot find pysam
updated 5.5 years ago by 45k • written 8.2 years ago by ▴ 480
0
votes
0
replies
9.6k
views
Comment: C: htseq-count cannot find pysam
updated 5.5 years ago by 45k • written 8.3 years ago by ▴ 480
2
votes
0
replies
1.9k
views
Answer: A: Retrotransposon analysis on ChIP-seq data.
updated 5.6 years ago by 45k • written 10.0 years ago by ▴ 480
1
vote
1
reply
4.2k
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Comment: C: RNA-seq: how big should be the library?
updated 5.7 years ago by 45k • written 10.1 years ago by ▴ 480
6
votes
7
replies
7.6k
views
What sequences should I use for ATAC-Seq adapter trimming using trimmomatic 0.36?
ATAC-Seq Trimmomatic Adapter Trimming
updated 6.3 years ago by 35k • written 6.3 years ago by ▴ 480
0
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1
reply
7.6k
views
Comment: C: What sequences should I use for ATAC-Seq adapter trimming using trimmomatic 0.36
6.3 years ago by Gary ▴ 480
0
votes
0
replies
7.6k
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Comment: C: What sequences should I use for ATAC-Seq adapter trimming using trimmomatic 0.36
6.3 years ago by Gary ▴ 480
0
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0
replies
11k
views
Comment: C: A weird PCA result using a local Galaxy
6.3 years ago by Gary ▴ 480
5
votes
4
replies
11k
views
A weird PCA result using a local Galaxy
RNA-Seq PCA Principal component analysis Galaxy
updated 6.3 years ago by 105k • written 6.3 years ago by ▴ 480
5
votes
3
replies
2.8k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
featureCounts minMQS quantification RNA-Seq
updated 6.4 years ago by ★ 8.1k • written 6.4 years ago by ▴ 480
0
votes
1
reply
3.5k
views
Comment: C: Duplicated ATAC-Seq peaks called by MACS2
6.4 years ago by Gary ▴ 480
7
votes
5
replies
3.5k
views
Duplicated ATAC-Seq peaks called by MACS2
MACS MACS2 ATAC-Seq peak calling
updated 6.4 years ago by 12k • written 6.4 years ago by ▴ 480
0
votes
1
reply
3.5k
views
Comment: C: Duplicated ATAC-Seq peaks called by MACS2
6.4 years ago by Gary ▴ 480
2
votes
1
reply
3.8k
views
Error message produced by bowtie2 (HiC-Pro)
bowtie2 HiC-Pro HiChIP alignment
updated 7.6 years ago by ▴ 10 • written 8.0 years ago by ▴ 480
2
votes
3
replies
4.3k
views
Bowtie2-build cannot build an index
Bowtie2 index
updated 7.6 years ago by 20 • written 8.3 years ago by ▴ 480
0
votes
0
replies
9.6k
views
Comment: C: htseq-count cannot find pysam
8.3 years ago by Gary ▴ 480
0
votes
0
replies
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
8.3 years ago by Gary ▴ 480
0
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1
reply
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
8.3 years ago by Gary ▴ 480
0
votes
2
replies
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
8.3 years ago by Gary ▴ 480
0
votes
0
replies
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
updated 8.3 years ago by 152k • written 8.3 years ago by ▴ 480
0
votes
2
replies
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
updated 8.3 years ago by 152k • written 8.3 years ago by ▴ 480
0
votes
1
reply
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
8.3 years ago by Gary ▴ 480
0
votes
0
replies
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
8.3 years ago by Gary ▴ 480
0
votes
0
replies
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
8.3 years ago by Gary ▴ 480
0
votes
3
replies
6.1k
views
Comment: C: Error of bam-to-sam conversion using samtools
8.3 years ago by Gary ▴ 480
13
votes
24
replies
6.1k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 8.3 years ago by 152k • written 8.3 years ago by ▴ 480
0
votes
1
reply
4.3k
views
Comment: C: Bowtie2-build cannot build an index
updated 8.3 years ago by 152k • written 8.3 years ago by ▴ 480
0
votes
0
replies
5.0k
views
Answer: A: Macs2 callpeak error: IndexError: list index out of range
8.5 years ago by Gary ▴ 480
0
votes
2
replies
5.0k
views
Macs2 callpeak error: IndexError: list index out of range
macs2 samtools bowtie2 ATAC-seq
8.5 years ago by Gary ▴ 480
3
votes
1
reply
4.3k
views
The scores of 5th column (integer score for display) in macs2 NAME_peaks.narrowPeak file are larger than 1000
ChIP-Seq macs2 UCSC Genome Browser bedToBigBed bed
updated 8.5 years ago by ▴ 580 • written 8.6 years ago by ▴ 480
0
votes
0
replies
1.7k
views
Abnormal coverage profile
RNA-Seq Qualimap Quality RNA degradation
8.9 years ago by Gary ▴ 480
0
votes
1
reply
3.5k
views
Comment: C: Failed FastQC Per sequence GC content of MeDIP Input sample
9.4 years ago by Gary ▴ 480
0
votes
4
replies
3.5k
views
Failed FastQC Per sequence GC content of MeDIP Input sample
MeDIP-Seq FastQC
updated 2.9 years ago by 45k • written 9.4 years ago by ▴ 480
0
votes
0
replies
4.0k
views
Answer: A: a question about some "basic numbers" for rna-seq experiments
10.0 years ago by Gary ▴ 480
0
votes
0
replies
2.7k
views
Comment: C: why only small fraction of reads from control sample of chip-seq are mapping int
10.0 years ago by Gary ▴ 480
2
votes
1
reply
5.5k
views
Answer: A: Functional Annotation of Tomato Transcriptome
10.0 years ago by Gary ▴ 480
0
votes
0
replies
5.9k
views
Comment: C: RNA-SEQ DEG -- No Control
10.0 years ago by Gary ▴ 480
1
vote
0
replies
4.8k
views
Answer: Answer: What's the best way to find all the possible cutting sites of an sequence-specif
updated 2.5 years ago by 45k • written 10.0 years ago by ▴ 480
0
votes
1
reply
4.0k
views
Answer: A: ChIP-Seq contaminated by human tissue?
10.0 years ago by Gary ▴ 480
8
votes
8
replies
4.0k
views
ChIP-Seq contaminated by human tissue?
ChIP-Seq
updated 2.5 years ago by 45k • written 10.0 years ago by ▴ 480
11
votes
1
reply
10.0k
views
Answer: Answer: How is FDR calculated in MACS?
updated 2.5 years ago by 45k • written 10.0 years ago by ▴ 480
1
vote
1
reply
5.3k
views
Answer: Answer: Reason for low mapping rate for murine RNA-seq data with splice-aware aligner?
updated 2.5 years ago by 45k • written 10.0 years ago by ▴ 480
1
vote
0
replies
5.6k
views
Answer: Answer: Differential expression without technical replicates
updated 2.5 years ago by 45k • written 10.0 years ago by ▴ 480
0
votes
1
reply
3.5k
views
Answer: A: Unexpected RNASeq result in shRNA experiment
10.1 years ago by Gary ▴ 480
0
votes
0
replies
4.7k
views
Answer: Answer: 48 Replicate RNA-Seq Study Points to Replicates Needed for DGE
updated 2.4 years ago by 45k • written 10.1 years ago by ▴ 480
1
vote
0
replies
6.7k
views
Comment: Comment: How to normalize gene expression values for finding similar genes
updated 2.9 years ago by 45k • written 10.1 years ago by ▴ 480
2
votes
2
replies
11k
views
Answer: Answer: Chip-Seq - Peak caller for broad enrichment of histone modifications?
updated 3.0 years ago by 45k • written 10.2 years ago by ▴ 480
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