Showing : bam • reset
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
1
vote
13
replies
2.5k
views
Rsamtools memory leak
rsamtools scanbam bam granges iranges
8.5 years ago mhills ▴ 10
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
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
5
votes
8
replies
6.0k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
9.2 years ago ben.ward ▴ 30
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
7
replies
1.8k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
9.1 years ago gen ▴ 30
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
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
1
vote
6
replies
2.2k
views
Detect short tandem repetitions from bam file
bam short tandem repetitions package
8.5 years ago Pau Marc Muñoz Torres ▴ 20
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
5
replies
1.4k
views
Graphing coverage() results
ggbio genomicalignments bam
9.2 years ago gen ▴ 30
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
3
votes
5
replies
2.7k
views
Split a BAM file with read groups
readgroup bam Rsamtools
3.1 years ago sbcn ▴ 80
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
2
votes
5
replies
1.9k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz bam pacbio
updated 7.9 years ago by ★ 1.6k • written 8.0 years ago by • 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
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
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
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
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
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
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
3
votes
3
replies
2.2k
views
about VCF and BAM files
SNV BAM
8.0 years ago Bogdan ▴ 670
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
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
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
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
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
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 7.7 years ago by • 0
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
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
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
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
0
votes
1
reply
144
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 22 days ago by 65k • written 22 days 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
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
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
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
1
reply
2.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
8.5 years ago eli7javasky • 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
4
votes
1
reply
4.6k
views
Rsubread featureCounts with strand information
Rsubread bam rnaseq
updated 7.3 years ago by ★ 28k • written 7.4 years ago by ▴ 110
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
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
0
votes
1
reply
1.4k
views
Consensus sequence from BAM file
consensus BAM
updated 4.5 years ago by 16k • written 4.5 years ago by • 0
1
vote
1
reply
577
views
r3cseq error with trimmed sequence as input
r3cseq bam trimmed
4.0 years ago ch_el ▴ 10
0
votes
0
replies
886
views
pairwise dist from bam file
bam diversity distance pairwise
6.6 years ago achaillon • 0
0
votes
0
replies
811
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
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Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient by JKim • 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
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SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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