Showing : bam • reset
1
vote
6
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2.2k
views
Detect short tandem repetitions from bam file
bam short tandem repetitions package
8.5 years ago Pau Marc Muñoz Torres ▴ 20
7
votes
4
replies
7.0k
views
how can I tell if a RNAseq BAM file is paired end or single end ?
NGS BAm
updated 9.4 years ago by ▴ 390 • written 9.4 years ago by ▴ 50
0
votes
20
replies
6.1k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 8.8 years ago by ▴ 90 • written 8.8 years ago by ▴ 10
4
votes
4
replies
2.4k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup rsamtools bam genomicalignments
updated 8.9 years ago by ▴ 180 • written 8.9 years ago by • 0
4
votes
5
replies
2.3k
views
scanBam on BamSampler supposed to be fast?
rsamtools bam
updated 9.3 years ago by 25k • written 9.3 years ago by ★ 2.0k
8
votes
3
replies
1.5k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 110
3
votes
3
replies
2.2k
views
about VCF and BAM files
SNV BAM
8.0 years ago Bogdan ▴ 670
5
votes
9
replies
2.2k
views
Reading alignments above a mapq threshold from BAM files
rsamtools bam
updated 8.8 years ago by 25k • written 8.8 years ago by ★ 2.0k
4
votes
4
replies
3.4k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.2 years ago by ▴ 20
1
vote
2
replies
2.2k
views
Processing bam files by read group
rsamtools read group bam
updated 9.3 years ago by ▴ 180 • written 9.5 years ago by ▴ 90
0
votes
5
replies
1.4k
views
Graphing coverage() results
ggbio genomicalignments bam
9.2 years ago gen ▴ 30
2
votes
5
replies
1.9k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz bam pacbio
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by • 0
0
votes
1
reply
1.2k
views
Reading BAM file for RapidR
RapidR BAM
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
2
votes
1
reply
4.0k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam rsamtools samtools genomicalignments
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 80
1
vote
1
reply
1.4k
views
Conversion of BSgenome format to GRanges format?
bsgenome granges bam
updated 9.2 years ago by 65k • written 9.2 years ago by • 0
3
votes
1
reply
1.9k
views
Is it possible to plot a track for each read group in a bam file with gviz without splitting the bam file into saparate bams?
gviz bam
updated 9.5 years ago by 25k • written 9.5 years ago by ▴ 90
6
votes
11
replies
3.0k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 9.5 years ago by ▴ 180 • written 9.5 years ago by ▴ 40
5
votes
8
replies
6.1k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
9.2 years ago ben.ward ▴ 30
1
vote
1
reply
1.1k
views
removing reads from coverage() calculation.
bam rsamtools genomicranges
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 30
0
votes
7
replies
1.8k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
9.1 years ago gen ▴ 30
4
votes
2
replies
1.5k
views
Slice of aligned sequences
bam granges genomicalignments
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 10
2
votes
2
replies
1.4k
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 10
0
votes
5
replies
2.1k
views
GAlignments and the query sequence (SEQ) field of BAM files
[galignments] bam
8.5 years ago Robert K. Bradley ▴ 40
1
vote
13
replies
2.6k
views
Rsamtools memory leak
rsamtools scanbam bam granges iranges
8.5 years ago mhills ▴ 10
3
votes
3
replies
1.6k
views
Read in specific rows of a BAM file that match a certain RNAME
scanbamparam bam
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 50
1
vote
5
replies
1.7k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
0
votes
1
reply
2.1k
views
Plotting coverage from bam files
bam plot
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 40
1
vote
2
replies
1.2k
views
Speed and memory of custom function using scanBam
rsamtools scanbamparam bam
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 510
7
votes
4
replies
3.2k
views
Convert BAM to FASTQ
BAM FASTQ
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 30
0
votes
1
reply
639
views
GUIDEseq bam input
GUIDEseq bam
updated 4.7 years ago by ★ 4.3k • written 4.7 years ago by ▴ 10
4
votes
6
replies
1.6k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 4.5 years ago by ▴ 740 • written 4.5 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Consensus sequence from BAM file
consensus BAM
updated 4.5 years ago by 16k • written 4.5 years ago by • 0
3
votes
5
replies
2.7k
views
Split a BAM file with read groups
readgroup bam Rsamtools
3.1 years ago sbcn ▴ 80
1
vote
3
replies
1.3k
views
issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by ▴ 10
0
votes
1
reply
147
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 24 days ago by 65k • written 24 days ago by • 0
1
vote
3
replies
1.4k
views
CopywriteR can't finish calculating copy number
copywriter bam
updated 7.9 years ago by ▴ 170 • written 7.9 years ago by • 0
3
votes
2
replies
1.6k
views
Plotting only intergenic reads on chromosomes?
gviz GenomeGraphs BAM rsamtools samtools
updated 7.7 years ago by 25k • written 7.8 years ago by • 0
4
votes
1
reply
4.6k
views
Rsubread featureCounts with strand information
Rsubread bam rnaseq
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 110
4
votes
2
replies
1.6k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 7.3 years ago by • 0 • written 7.3 years ago by ▴ 40
3
votes
6
replies
1.7k
views
Whole exome: BAM statistics and other relevant information
rsamtools whole exome sequence bam exome R
7.2 years ago bioinf ▴ 10
1
vote
4
replies
2.0k
views
Gviz sashimi read count
Gviz sashimi sashimi plots read counting bam
updated 7.2 years ago by ▴ 730 • written 7.2 years ago by • 0
1
vote
2
replies
1.5k
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
2
votes
8
replies
2.0k
views
CAGEr BAM files size issue
CAGEr BAM software error R biostrings
updated 6.7 years ago by ▴ 180 • written 6.8 years ago by ▴ 10
0
votes
1
reply
2.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
8.5 years ago eli7javasky • 0
0
votes
0
replies
502
views
Prepare data frame of 3 column-lists or matrix of three-column lists from VCF or BAM files
BAM Segmentation CINdex VCF Data
20 months ago raven1306 • 0
0
votes
1
reply
1.2k
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
9.1 years ago gen ▴ 30
0
votes
0
replies
814
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER HiCUP BAM HiC
2.4 years ago Ankit ▴ 20
0
votes
0
replies
1.0k
views
filter and trim large fasta/bam files
deep sequencing fasta bam trim
6.6 years ago achaillon • 0
0
votes
0
replies
888
views
pairwise dist from bam file
bam diversity distance pairwise
6.6 years ago achaillon • 0
0
votes
4
replies
1.6k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments bam scanbamparam
7.3 years ago mikko.arvas • 0
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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