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Rank
Views
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Showing :
BAM
•
reset
0
votes
0
replies
180
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER
HiCUP
BAM
HiC
8 months ago
Ankit
▴ 10
1
vote
3
replies
467
views
issue with DiffBind dba.count
bam
bai
DiffBind
dba.count
Diffbind
updated 11 months ago by
Rory Stark
★ 4.4k • written 12 months ago by
mtsompana
▴ 10
3
votes
5
replies
1.0k
views
Split a BAM file with read groups
readgroup
bam
Rsamtools
16 months ago
sbcn
▴ 80
1
vote
3
replies
948
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
17 months ago
changxu.fan
▴ 10
1
vote
1
reply
242
views
r3cseq error with trimmed sequence as input
r3cseq
bam
trimmed
2.3 years ago
ch_el
▴ 10
0
votes
1
reply
459
views
Consensus sequence from BAM file
consensus
BAM
updated 2.7 years ago by
Hervé Pagès
15k • written 2.8 years ago by
O. William McClung
• 0
4
votes
6
replies
695
views
How to query a base along an aligned read by genomic position?
GenomicAlignments
BAM
CIGAR
updated 2.8 years ago by
Janet Young
▴ 740 • written 2.8 years ago by
Shian Su
▴ 40
0
votes
1
reply
300
views
GUIDEseq bam input
GUIDEseq
bam
updated 3.0 years ago by
Julie Zhu
★ 4.3k • written 3.0 years ago by
tomas.rodriguez
▴ 10
7
votes
4
replies
1.7k
views
Convert BAM to FASTQ
BAM
FASTQ
updated 3.4 years ago by
Martin Morgan
25k • written 3.4 years ago by
ioannis.vardaxis
▴ 30
1
vote
2
replies
669
views
Speed and memory of custom function using scanBam
rsamtools
scanbamparam
bam
updated 3.9 years ago by
Martin Morgan
25k • written 3.9 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
1
reply
1.2k
views
Plotting coverage from bam files
bam
plot
updated 4.3 years ago by
James W. MacDonald
60k • written 4.3 years ago by
gv
▴ 40
0
votes
0
replies
752
views
Rsamtools insert size
rsamtools
samtools
bam
bowtie2
4.5 years ago
igor
▴ 40
0
votes
0
replies
535
views
pairwise dist from bam file
bam
diversity
distance
pairwise
4.8 years ago
achaillon
• 0
0
votes
0
replies
584
views
filter and trim large fasta/bam files
deep sequencing
fasta
bam
trim
4.8 years ago
achaillon
• 0
2
votes
8
replies
1.3k
views
CAGEr BAM files size issue
CAGEr
BAM
software error
R
biostrings
updated 5.0 years ago by
Charles Plessy
▴ 170 • written 5.1 years ago by
orzechowska.mag
▴ 10
1
vote
2
replies
961
views
Gviz off-by-one with STAR BAM
gviz
off-by-one
STAR
BAM
coverage
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
bernt.popp
• 0
1
vote
4
replies
1.3k
views
Gviz sashimi read count
Gviz
sashimi
sashimi plots
read counting
bam
updated 5.4 years ago by
Robert Ivanek
▴ 730 • written 5.4 years ago by
bernt.popp
• 0
3
votes
6
replies
1.0k
views
Whole exome: BAM statistics and other relevant information
rsamtools
whole exome sequence
bam
exome
R
5.5 years ago
bioinf
▴ 10
4
votes
2
replies
1.1k
views
bamsignals - bamcoverage has no strand-specific option??
BAM
bamsignals
Coverage
updated 5.5 years ago by
helmuth
• 0 • written 5.6 years ago by
gtho123
▴ 40
0
votes
4
replies
1.2k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments
bam
scanbamparam
5.5 years ago
mikko.arvas
• 0
4
votes
1
reply
3.6k
views
Rsubread featureCounts with strand information
Rsubread
bam
rnaseq
updated 5.6 years ago by
Aaron Lun
★ 27k • written 5.6 years ago by
rubi
▴ 100
3
votes
2
replies
1.0k
views
Plotting only intergenic reads on chromosomes?
gviz
GenomeGraphs
BAM
rsamtools
samtools
updated 6.0 years ago by
Martin Morgan
25k • written 6.0 years ago by
Mehmet Ilyas Cosacak
• 0
8
votes
3
replies
936
views
Counting ambiguously mapped reads per feature
rnaseq
bam
genomicranges
GenomicAlignments
Rsamtools
updated 6.1 years ago by
Gordon Smyth
46k • written 6.1 years ago by
rubi
▴ 100
1
vote
3
replies
862
views
CopywriteR can't finish calculating copy number
copywriter
bam
updated 6.2 years ago by
t.kuilman
170 • written 6.2 years ago by
thestaroceanster
• 0
2
votes
5
replies
1.2k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz
bam
pacbio
updated 6.2 years ago by
florian.hahne@novartis.com
★ 1.6k • written 6.2 years ago by
thackl
• 0
2
votes
1
reply
2.7k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam
rsamtools
samtools
genomicalignments
updated 6.3 years ago by
Martin Morgan
25k • written 6.3 years ago by
Vang Le
▴ 70
3
votes
3
replies
1.5k
views
about VCF and BAM files
SNV
BAM
6.3 years ago
Bogdan
▴ 640
0
votes
1
reply
924
views
Reading BAM file for RapidR
RapidR
BAM
updated 6.4 years ago by
Aaron Lun
★ 27k • written 6.4 years ago by
Sushant Pawar
• 0
0
votes
5
replies
1.2k
views
diffHic preparePairs() does not identify paired-end reads
diffHic
preparePairs
paired
BAM
updated 6.5 years ago by
Aaron Lun
★ 27k • written 6.5 years ago by
ilyco
• 0
3
votes
3
replies
1.1k
views
Read in specific rows of a BAM file that match a certain RNAME
scanbamparam
bam
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
K
▴ 50
1
vote
6
replies
1.4k
views
Detect short tandem repetitions from bam file
bam
short tandem repetitions
package
6.8 years ago
Pau Marc Muñoz Torres
▴ 20
0
votes
1
reply
1.7k
views
diffBind - bam not accessible
diffbind
chip-seq
bam
6.8 years ago
eli7javasky
• 0
1
vote
13
replies
1.8k
views
Rsamtools memory leak
rsamtools
scanbam
bam
granges
iranges
6.8 years ago
mhills
▴ 10
0
votes
5
replies
1.4k
views
GAlignments and the query sequence (SEQ) field of BAM files
[galignments]
bam
6.8 years ago
Robert K. Bradley
▴ 40
2
votes
2
replies
988
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error
easyrnaseq
genomicalignments
bam
updated 6.9 years ago by
Martin Morgan
25k • written 6.9 years ago by
Michael Dondrup
▴ 10
0
votes
20
replies
4.7k
views
SummarizeOverlaps in R
summarizeoverlaps
Bam
rstudio
updated 7.1 years ago by
Jake
▴ 90 • written 7.1 years ago by
Lillyhchen
▴ 10
5
votes
9
replies
1.6k
views
Reading alignments above a mapq threshold from BAM files
rsamtools
bam
updated 7.1 years ago by
Martin Morgan
25k • written 7.1 years ago by
Johannes Rainer
★ 2.0k
4
votes
2
replies
961
views
Slice of aligned sequences
bam
granges
genomicalignments
updated 7.1 years ago by
Hervé Pagès
15k • written 7.1 years ago by
Thomas Poulsen
▴ 10
4
votes
4
replies
1.8k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup
rsamtools
bam
genomicalignments
updated 7.1 years ago by
Nathaniel Hayden
▴ 180 • written 7.2 years ago by
Sam Buckberry
• 0
0
votes
1
reply
806
views
Mean Coverage version of stat_coverage and coverage?
grangeslist
granges
Genomicfeatures
bam
7.4 years ago
gen
▴ 30
0
votes
7
replies
1.2k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges
reads
genomicfeatures
Bam
7.4 years ago
gen
▴ 30
0
votes
5
replies
963
views
Graphing coverage() results
ggbio
genomicalignments
bam
7.5 years ago
gen
▴ 30
1
vote
1
reply
867
views
removing reads from coverage() calculation.
bam
rsamtools
genomicranges
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
gen
▴ 30
5
votes
8
replies
4.6k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam
sam
alignment
biostrings
7.5 years ago
ben.ward
▴ 30
1
vote
1
reply
1.0k
views
Conversion of BSgenome format to GRanges format?
bsgenome
granges
bam
updated 7.5 years ago by
James W. MacDonald
60k • written 7.5 years ago by
pterry
• 0
4
votes
5
replies
1.6k
views
scanBam on BamSampler supposed to be fast?
rsamtools
bam
updated 7.6 years ago by
Martin Morgan
25k • written 7.6 years ago by
Johannes Rainer
★ 2.0k
1
vote
2
replies
1.7k
views
Processing bam files by read group
rsamtools
read group
bam
updated 7.6 years ago by
Nathaniel Hayden
▴ 180 • written 7.8 years ago by
Thomas Sandmann
▴ 80
7
votes
4
replies
5.3k
views
how can I tell if a RNAseq BAM file is paired end or single end ?
NGS
BAm
updated 7.6 years ago by
Sonali Arora
▴ 380 • written 7.7 years ago by
stephen66
▴ 50
6
votes
11
replies
2.0k
views
Comparing read sequence back to reference sequence
bam
indel
genomicalignments
biostrings
updated 7.7 years ago by
Nathaniel Hayden
▴ 180 • written 7.7 years ago by
Stefanie Tauber
▴ 40
3
votes
1
reply
1.5k
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 7.8 years ago by
Martin Morgan
25k • written 7.8 years ago by
Pablo marin-garcia
▴ 90
50 results • Page
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Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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