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350
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ChIPQC read depth doesn't match BAM files
ChIPseq ChIPQC
updated 10 months ago by ★ 1.7k • written 10 months ago by ▴ 10
1
vote
1
reply
680
views
DiffBind - Comparing normalization/background methods - how to create a heatmap (as in 7.5)?
DiffBind normalization ChIPseq
updated 13 months ago by ★ 1.7k • written 13 months ago by ▴ 10
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0
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602
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Comment: Comment: help for dba.count settings for RNAPII-ChIP using GRanges peakset
15 months ago by bertb ▴ 10
1
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2
replies
602
views
help for dba.count settings for RNAPII-ChIP using GRanges peakset
DiffBind ChIPseq
15 months ago by bertb ▴ 10
0
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0
replies
912
views
Comment: Comment: Problems with dba.analyze in DiffBind - are blacklists/greylists required to obt
15 months ago by bertb ▴ 10
3
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2
replies
912
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Problems with dba.analyze in DiffBind - are blacklists/greylists required to obtain DESeq sites?
blacklist dba.analyze ChIPseq greylist diffbind
15 months ago by bertb ▴ 10
0
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0
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605
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Comment: Comment: DiffBind normalization returned NULL
15 months ago by bertb ▴ 10
2
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2
replies
605
views
DiffBind normalization returned NULL
DiffBind dba.normalize normalization ChIPseq
15 months ago by bertb ▴ 10
0
votes
1
reply
710
views
Comment: C: error when running NGS tools in bash script
2.5 years ago by bertb ▴ 10
0
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4
replies
710
views
error when running NGS tools in bash script
software error automation scripting
2.5 years ago by bertb ▴ 10
3
votes
10
replies
2.1k
views
how to identify where multi-mappers, or "non primary hits" are mapping to
RNA-Seq alignment next-gen
updated 2.5 years ago by 20 • written 2.6 years ago by ▴ 10
0
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0
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641
views
bam_stat.py and featureCounts stats don't seem to make sense (to me)
RNA-Seq alignment
2.6 years ago by bertb ▴ 10
0
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0
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2.8k
views
Comment: C: How to filter out chromosome regions from a .bam file
2.6 years ago by bertb ▴ 10
8
votes
4
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2.8k
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How to filter out chromosome regions from a .bam file
RNA-Seq alignment
updated 2.6 years ago by 2.9k • written 2.6 years ago by ▴ 10
0
votes
0
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523
views
How to unique mappers become concordant pairs aligned >1 times
RNA-Seq alignment
2.6 years ago by bertb ▴ 10
0
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0
replies
2.1k
views
Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
2.6 years ago by bertb ▴ 10
0
votes
1
reply
2.1k
views
Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
2.6 years ago by bertb ▴ 10
0
votes
1
reply
2.1k
views
Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
2.6 years ago by bertb ▴ 10
0
votes
1
reply
2.1k
views
Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
2.6 years ago by bertb ▴ 10
0
votes
0
replies
1.3k
views
Comment: C: featureCount with high multimapping fragments
2.6 years ago by bertb ▴ 10
0
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0
replies
958
views
Comment: C: Picard CreateSequenceDictionary - file doesn't look right?
2.6 years ago by bertb ▴ 10
0
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1
reply
958
views
Comment: C: Picard CreateSequenceDictionary - file doesn't look right?
2.6 years ago by bertb ▴ 10
1
vote
6
replies
958
views
Picard CreateSequenceDictionary - file doesn't look right?
RNA-Seq sequencing
updated 2.6 years ago by 20 • written 2.6 years ago by ▴ 10
0
votes
1
reply
958
views
Comment: C: Picard CreateSequenceDictionary - file doesn't look right?
2.6 years ago by bertb ▴ 10
0
votes
1
reply
1.3k
views
Comment: C: featureCount with high multimapping fragments
2.7 years ago by bertb ▴ 10
0
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4
replies
1.3k
views
featureCount with high multimapping fragments
RNA-Seq sequencing
updated 2.7 years ago by 13k • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Comment: C: htseq_counts process "Killed" during SAM alignment record pairs processed
2.7 years ago by bertb ▴ 10
0
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3
replies
1.1k
views
htseq_counts process "Killed" during SAM alignment record pairs processed
RNA-Seq next-gen
2.7 years ago by bertb ▴ 10
0
votes
0
replies
745
views
Comment: C: Errors with Picard CollectRnaSeqMetrics
2.7 years ago by bertb ▴ 10
3
votes
2
replies
745
views
Errors with Picard CollectRnaSeqMetrics
RNA-Seq alignment software error
updated 2.7 years ago by 154k • written 2.7 years ago by ▴ 10
0
votes
0
replies
978
views
Comment: C: check_strandedness error with how_are_we_stranded_here tool
2.7 years ago by bertb ▴ 10
0
votes
1
reply
978
views
Comment: C: check_strandedness error with how_are_we_stranded_here tool
2.7 years ago by bertb ▴ 10
1
vote
4
replies
978
views
check_strandedness error with how_are_we_stranded_here tool
RNA-Seq sequencing assembly
2.7 years ago by bertb ▴ 10
0
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1
reply
841
views
Comment: C: how_are_we_stranded_here install issue on Xubuntu
2.7 years ago by bertb ▴ 10
0
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0
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841
views
Comment: C: how_are_we_stranded_here install issue on Xubuntu
2.7 years ago by bertb ▴ 10
4
votes
5
replies
841
views
how_are_we_stranded_here install issue on Xubuntu
RNA-Seq sequencing Assembly
updated 2.7 years ago by 39k • written 2.7 years ago by ▴ 10
0
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1
reply
3.1k
views
Comment: C: MACS2 won't build model - too few paired peaks, but I'm not using paired data
4.5 years ago by bertb ▴ 10
0
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0
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3.1k
views
Comment: C: MACS2 won't build model - too few paired peaks, but I'm not using paired data
4.5 years ago by bertb ▴ 10
0
votes
5
replies
3.1k
views
MACS2 won't build model - too few paired peaks, but I'm not using paired data
ChIP-Seq
4.5 years ago by bertb ▴ 10
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