Showing : BAM • reset
0
votes
1
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559
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
0
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803
views
Prepare data frame of 3 column-lists or matrix of three-column lists from VCF or BAM files
BAM Segmentation CINdex VCF Data
3.0 years ago raven1306 • 0
0
votes
0
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1.3k
views
How to prepare HiCUP BAM output as input for HOMER?
HOMER HiCUP BAM HiC
3.8 years ago Ankit ▴ 20
1
vote
3
replies
1.8k
views
issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 4.0 years ago by ★ 5.2k • written 4.1 years ago by ▴ 10
3
votes
5
replies
3.7k
views
Split a BAM file with read groups
readgroup bam Rsamtools
4.4 years ago sbcn ▴ 80
4
votes
4
replies
5.3k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 4.5 years ago by ▴ 20
1
vote
1
reply
866
views
r3cseq error with trimmed sequence as input
r3cseq bam trimmed
5.4 years ago ch_el ▴ 10
0
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1
reply
2.0k
views
Consensus sequence from BAM file
consensus BAM
updated 5.8 years ago by 16k • written 5.8 years ago by • 0
4
votes
6
replies
2.5k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 5.8 years ago by ▴ 740 • written 5.8 years ago by ▴ 40
0
votes
1
reply
895
views
GUIDEseq bam input
GUIDEseq bam
updated 6.1 years ago by ★ 4.3k • written 6.1 years ago by ▴ 10
7
votes
4
replies
4.3k
views
Convert BAM to FASTQ
BAM FASTQ
updated 6.4 years ago by 25k • written 6.4 years ago by ▴ 30
1
vote
2
replies
1.5k
views
Speed and memory of custom function using scanBam
rsamtools scanbamparam bam
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 510
0
votes
1
reply
3.1k
views
Plotting coverage from bam files
bam plot
updated 7.3 years ago by 68k • written 7.3 years ago by ▴ 40
0
votes
0
replies
1.6k
views
Rsamtools insert size
rsamtools samtools bam bowtie2
7.6 years ago igor ▴ 50
0
votes
0
replies
1.2k
views
pairwise dist from bam file
bam diversity distance pairwise
7.9 years ago achaillon • 0
0
votes
0
replies
1.4k
views
filter and trim large fasta/bam files
deep sequencing fasta bam trim
7.9 years ago achaillon • 0
2
votes
8
replies
2.6k
views
CAGEr BAM files size issue
CAGEr BAM software error R biostrings
updated 8.1 years ago by ▴ 180 • written 8.1 years ago by ▴ 10
1
vote
2
replies
1.9k
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 8.5 years ago by 25k • written 8.5 years ago by • 0
1
vote
4
replies
2.6k
views
Gviz sashimi read count
Gviz sashimi sashimi plots read counting bam
updated 8.5 years ago by ▴ 750 • written 8.5 years ago by • 0
3
votes
6
replies
2.2k
views
Whole exome: BAM statistics and other relevant information
rsamtools whole exome sequence bam exome R
8.6 years ago bioinf ▴ 10
4
votes
2
replies
2.0k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 8.6 years ago by • 0 • written 8.6 years ago by ▴ 40
0
votes
4
replies
2.0k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments bam scanbamparam
8.6 years ago mikko.arvas • 0
4
votes
1
reply
5.3k
views
Rsubread featureCounts with strand information
Rsubread bam rnaseq
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 110
3
votes
2
replies
1.9k
views
Plotting only intergenic reads on chromosomes?
gviz GenomeGraphs BAM rsamtools samtools
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
8
votes
3
replies
1.9k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 9.1 years ago by 52k • written 9.1 years ago by ▴ 110
1
vote
3
replies
1.8k
views
CopywriteR can't finish calculating copy number
copywriter bam
updated 9.3 years ago by ▴ 170 • written 9.3 years ago by • 0
2
votes
5
replies
2.6k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz bam pacbio
updated 9.3 years ago by ★ 1.6k • written 9.3 years ago by • 0
2
votes
1
reply
5.1k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam rsamtools samtools genomicalignments
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 80
3
votes
3
replies
2.7k
views
about VCF and BAM files
SNV BAM
9.4 years ago Bogdan ▴ 670
0
votes
1
reply
1.5k
views
Reading BAM file for RapidR
RapidR BAM
updated 9.5 years ago by ★ 29k • written 9.5 years ago by • 0
1
vote
5
replies
2.2k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
3
votes
3
replies
2.2k
views
Read in specific rows of a BAM file that match a certain RNAME
scanbamparam bam
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 50
1
vote
6
replies
2.9k
views
Detect short tandem repetitions from bam file
bam short tandem repetitions package
9.9 years ago Pau Marc Muñoz Torres ▴ 20
0
votes
1
reply
3.0k
views
diffBind - bam not accessible
diffbind chip-seq bam
9.9 years ago eli7javasky • 0
1
vote
13
replies
3.2k
views
Rsamtools memory leak
rsamtools scanbam bam granges iranges
9.9 years ago mhills ▴ 10
0
votes
5
replies
2.8k
views
GAlignments and the query sequence (SEQ) field of BAM files
[galignments] bam
9.9 years ago Robert K. Bradley ▴ 40
2
votes
2
replies
1.8k
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 10
0
votes
20
replies
7.7k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 10.1 years ago by ▴ 90 • written 10.1 years ago by ▴ 10
5
votes
9
replies
2.9k
views
Reading alignments above a mapq threshold from BAM files
rsamtools bam
updated 10.2 years ago by 25k • written 10.2 years ago by ★ 2.1k
4
votes
2
replies
1.8k
views
Slice of aligned sequences
bam granges genomicalignments
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 10
4
votes
4
replies
2.9k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup rsamtools bam genomicalignments
updated 10.2 years ago by ▴ 180 • written 10.2 years ago by • 0
0
votes
1
reply
1.4k
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
10.4 years ago gen ▴ 30
0
votes
7
replies
2.2k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
10.5 years ago • updated 10.4 years ago gen ▴ 30
0
votes
5
replies
1.8k
views
Graphing coverage() results
ggbio genomicalignments bam
10.5 years ago gen ▴ 30
1
vote
1
reply
1.5k
views
removing reads from coverage() calculation.
bam rsamtools genomicranges
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 30
5
votes
8
replies
7.1k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
10.6 years ago ben.ward ▴ 30
1
vote
1
reply
1.7k
views
Conversion of BSgenome format to GRanges format?
bsgenome granges bam
updated 10.6 years ago by 68k • written 10.6 years ago by • 0
4
votes
5
replies
2.7k
views
scanBam on BamSampler supposed to be fast?
rsamtools bam
updated 10.6 years ago by 25k • written 10.6 years ago by ★ 2.1k
1
vote
2
replies
2.8k
views
Processing bam files by read group
rsamtools read group bam
updated 10.7 years ago by ▴ 180 • written 10.8 years ago by ▴ 90
7
votes
4
replies
8.1k
views
how can I tell if a RNAseq BAM file is paired end or single end ?
NGS BAm
updated 10.7 years ago by ▴ 390 • written 10.7 years ago by ▴ 50
52 results • Page 1 of 2
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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