Showing : BAM • reset
0
votes
3
replies
153
views
issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 29 days ago by ★ 4.1k • written 6 weeks ago by • 0
3
votes
5
replies
316
views
Split a BAM file with read groups
readgroup bam Rsamtools
6 months ago • updated 5 months ago sbcn ▴ 70
1
vote
3
replies
278
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
6 months ago changxu.fan • 0
1
vote
1
reply
134
views
r3cseq error with trimmed sequence as input
r3cseq bam trimmed
17 months ago ch_el ▴ 10
0
votes
1
reply
201
views
Consensus sequence from BAM file
consensus BAM
updated 22 months ago by 15k • written 23 months ago by • 0
4
votes
6
replies
430
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 22 months ago by ▴ 740 • written 23 months ago by ▴ 40
0
votes
1
reply
197
views
GUIDEseq bam input
GUIDEseq bam
updated 2.1 years ago by ★ 4.3k • written 2.1 years ago by ▴ 10
7
votes
4
replies
944
views
Convert BAM to FASTQ
BAM FASTQ
updated 2.5 years ago by 25k • written 2.5 years ago by ▴ 30
1
vote
2
replies
523
views
Speed and memory of custom function using scanBam
rsamtools scanbamparam bam
updated 3.0 years ago by 25k • written 3.0 years ago by ▴ 480
0
votes
1
reply
920
views
Plotting coverage from bam files
bam plot
updated 3.4 years ago by 58k • written 3.4 years ago by ▴ 40
0
votes
0
replies
628
views
Rsamtools insert size
rsamtools samtools bam bowtie2
3.6 years ago igor ▴ 40
0
votes
0
replies
433
views
pairwise dist from bam file
bam diversity distance pairwise
3.9 years ago achaillon • 0
0
votes
0
replies
468
views
filter and trim large fasta/bam files
deep sequencing fasta bam trim
4.0 years ago achaillon • 0
2
votes
8
replies
929
views
CAGEr BAM files size issue
CAGEr BAM software error R biostrings
updated 4.1 years ago by ▴ 130 • written 4.2 years ago by ▴ 10
1
vote
2
replies
809
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
1
vote
4
replies
1.1k
views
Gviz sashimi read count
Gviz sashimi sashimi plots read counting bam
updated 4.5 years ago by ▴ 700 • written 4.6 years ago by • 0
3
votes
6
replies
870
views
Whole exome: BAM statistics and other relevant information
rsamtools whole exome sequence bam exome R
4.6 years ago bioinf ▴ 10
4
votes
2
replies
926
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 4.7 years ago by • 0 • written 4.7 years ago by ▴ 40
0
votes
4
replies
1.0k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments bam scanbamparam
4.7 years ago mikko.arvas • 0
4
votes
1
reply
3.1k
views
Rsubread featureCounts with strand information
Rsubread bam rnaseq
updated 4.7 years ago by ★ 27k • written 4.8 years ago by ▴ 90
3
votes
2
replies
843
views
Plotting only intergenic reads on chromosomes?
gviz GenomeGraphs BAM rsamtools samtools
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
8
votes
3
replies
782
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 90
1
vote
3
replies
708
views
CopywriteR can't finish calculating copy number
copywriter bam
updated 5.3 years ago by 170 • written 5.3 years ago by • 0
2
votes
5
replies
1.0k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz bam pacbio
updated 5.3 years ago by ★ 1.6k • written 5.4 years ago by • 0
2
votes
1
reply
2.4k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam rsamtools samtools genomicalignments
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 70
3
votes
3
replies
1.3k
views
about VCF and BAM files
SNV BAM
5.4 years ago Bogdan ▴ 620
0
votes
1
reply
837
views
Reading BAM file for RapidR
RapidR BAM
updated 5.5 years ago by ★ 27k • written 5.5 years ago by • 0
0
votes
5
replies
1.0k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 5.6 years ago by ★ 27k • written 5.6 years ago by • 0
3
votes
3
replies
961
views
Read in specific rows of a BAM file that match a certain RNAME
scanbamparam bam
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 50
1
vote
6
replies
1.2k
views
Detect short tandem repetitions from bam file
bam short tandem repetitions package
5.9 years ago Pau Marc Muñoz Torres ▴ 20
0
votes
1
reply
1.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
5.9 years ago eli7javasky • 0
1
vote
13
replies
1.6k
views
Rsamtools memory leak
rsamtools scanbam bam granges iranges
5.9 years ago mhills ▴ 10
0
votes
5
replies
1.2k
views
GAlignments and the query sequence (SEQ) field of BAM files
[galignments] bam
5.9 years ago Robert K. Bradley ▴ 40
2
votes
2
replies
863
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 6.0 years ago by 25k • written 6.0 years ago by ▴ 10
0
votes
20
replies
4.0k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 6.2 years ago by ▴ 90 • written 6.2 years ago by ▴ 10
5
votes
9
replies
1.5k
views
Reading alignments above a mapq threshold from BAM files
rsamtools bam
updated 6.2 years ago by 25k • written 6.2 years ago by ★ 1.9k
4
votes
2
replies
841
views
Slice of aligned sequences
bam granges genomicalignments
updated 6.2 years ago by 15k • written 6.2 years ago by ▴ 10
4
votes
4
replies
1.7k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup rsamtools bam genomicalignments
updated 6.3 years ago by ▴ 180 • written 6.3 years ago by • 0
0
votes
1
reply
723
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
6.5 years ago gen ▴ 30
0
votes
7
replies
1.1k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
6.5 years ago gen ▴ 30
0
votes
5
replies
858
views
Graphing coverage() results
ggbio genomicalignments bam
6.6 years ago gen ▴ 30
1
vote
1
reply
798
views
removing reads from coverage() calculation.
bam rsamtools genomicranges
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 30
5
votes
8
replies
3.9k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
6.6 years ago ben.ward ▴ 30
1
vote
1
reply
920
views
Conversion of BSgenome format to GRanges format?
bsgenome granges bam
updated 6.6 years ago by 58k • written 6.6 years ago by • 0
4
votes
5
replies
1.5k
views
scanBam on BamSampler supposed to be fast?
rsamtools bam
updated 6.7 years ago by 25k • written 6.7 years ago by ★ 1.9k
1
vote
2
replies
1.5k
views
Processing bam files by read group
rsamtools read group bam
updated 6.7 years ago by ▴ 180 • written 6.9 years ago by ▴ 80
7
votes
4
replies
4.7k
views
how can I tell if a RNAseq BAM file is paired end or single end ?
NGS BAm
updated 6.8 years ago by ▴ 380 • written 6.8 years ago by ▴ 50
6
votes
11
replies
1.7k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 6.9 years ago by ▴ 180 • written 6.9 years ago by ▴ 40
3
votes
1
reply
1.4k
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 6.9 years ago by 25k • written 6.9 years ago by ▴ 90
49 results • Page 1 of 1
Recent ...
Replies
Comment: Extracting normalized counts in MEDIPS by Lukas ▴ 10
Hi Ishepard, I am glad to hear that the quantile normalized values give you reasonable visualizations. The TMM normalization happens withi…
Comment: Extracting normalized counts in MEDIPS by lshepard ▴ 40
Hi Lukas, thank you for the quick reply! Understood on the warning. Makes sense now. Regarding visualization - simply put, yes on a "per …
Comment: Extracting normalized counts in MEDIPS by Lukas ▴ 10
Hi, Thanks for your inquiry! >When quantile normalization are selected: >Results table count have quantile normalized values, which is w…
Comment: Extracting normalized counts in MEDIPS by lshepard ▴ 40
Hello Lukas. Thank you for the reply. After coming back to this after a while and normalizing by quantile it seems like the counts are actu…
Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
If this is taking too long, you can run it on a subsample (e.g. hundreds of samples) to identify parameters for the VST, and then apply it …
Votes
Comment: Extracting normalized counts in MEDIPS
Comment: "full model matrix is less than full rank"
A: Extracting normalized counts in MEDIPS
Answer: "full model matrix is less than full rank"
Comment: Unique GPos taking into account mcols
Awards • All
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