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2
votes
4
replies
776
views
Computing pairwise AA global sequence alignment between all pairs in a vector of sequences
pairwiseAlignment
9 months ago by rubic ▴ 270
1
vote
3
replies
714
views
Gene set enrichment analysis for genetic interactions
gsea genetic-interactions
13 months ago by rubic ▴ 270
1
vote
1
reply
763
views
Handling NA values in limma's voom design matrix
rna-seq voom design.matrix limma NA
updated 2.0 years ago by 82k • written 2.0 years ago by ▴ 270
0
votes
1
reply
429
views
Extract primary STAR mapped reads to specific chromosomes
samtools STAR
updated 2.3 years ago by ★ 1.5k • written 2.3 years ago by ▴ 270
1
vote
1
reply
621
views
Quantifying expression levels of IsoSeq reads with Kallisto
IsoSeq Kallisto expression
updated 2.4 years ago by ★ 6.1k • written 2.4 years ago by ▴ 270
1
vote
2
replies
1.1k
views
Distinguishing between ambiguously mapped reads in a split bamToBed file
reads RNA-Seq bam bamToBed split
2.4 years ago by rubic ▴ 270
2
votes
1
reply
519
views
Extract the mapped portion of the read sequence
bam RNA-Seq cigar
updated 2.4 years ago by 82k • written 2.4 years ago by ▴ 270
2
votes
1
reply
590
views
Usage of bedTools
bedTools bamToBed
2.4 years ago by rubic ▴ 270
0
votes
0
replies
413
views
Extract overlapping sequences from a bam file
bam RNA-Seq split splicing cigar
2.4 years ago by rubic ▴ 270
1
vote
1
reply
781
views
Downloading the IMGT/V-QUEST software
vquest software
updated 16 months ago by ▴ 990 • written 2.5 years ago by ▴ 270
1
vote
0
replies
505
views
Biostrings readDNAStringSet handling of N bases
Biostrings
2.7 years ago by rubic ▴ 270
0
votes
0
replies
874
views
HLA haplotypes VCF
HLA Haplotype VCF
2.8 years ago by rubic ▴ 270
3
votes
5
replies
2.2k
views
Fast parsing genbank files
Genbank parsing R
updated 3.1 years ago by 100k • written 3.1 years ago by ▴ 270
0
votes
1
reply
989
views
Blast a CDD PSSM against a genome
pssm CDD blast
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 270
1
vote
3
replies
1.1k
views
Searching for conserved domains in a chromosome/scaffold
blast domain CDD PSSM rpsblast
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 270
1
vote
1
reply
959
views
Getting all the genomic coordinates where RNA-seq reads are split within a given genomic interval in a bam file
RNA-Seq bam splicing cigar reads
updated 3.4 years ago by 162k • written 3.4 years ago by ▴ 270
2
votes
1
reply
1.2k
views
GET Ensembl xrefs for multiple queries
ensembl httr api
updated 3.8 years ago by ★ 2.4k • written 3.8 years ago by ▴ 270
3
votes
5
replies
1.5k
views
Get Ensembl mapping between the chromosome and scaffold names
ensembl Assembly scaffold chromosome
updated 4.9 years ago by ▴ 290 • written 4.9 years ago by ▴ 270
1
vote
4
replies
1.6k
views
AGP files in Ensembl
Assembly AGP ensembl
updated 5.1 years ago by 23k • written 5.1 years ago by ▴ 270
0
votes
1
reply
1.0k
views
Parse sim4 output alignment format
sim4 pairwise alignment parse
5.3 years ago by rubic ▴ 270
2
votes
2
replies
1.7k
views
Error while building picard tools from broadinstitute-picard-a4d54b4
picard broad
updated 5.7 years ago by 44k • written 8.3 years ago by ▴ 270
0
votes
1
reply
1.3k
views
Getting transcriptomic coordinates for CDS exons from a GTF
GTF BED
6.1 years ago by rubic ▴ 270
1
vote
4
replies
1.6k
views
Running salmon after subsetting the bam to transcripts annotated as protein coding in the GTF
salmon samtools GTF gencode
6.1 years ago by rubic ▴ 270
1
vote
1
reply
1.9k
views
Does samtools view -b -h <input.bam> -L <input.bed> keep the original header?
samtools header
updated 6.1 years ago by ★ 2.9k • written 6.1 years ago by ▴ 270
0
votes
1
reply
1.1k
views
Number of sequenced positions from a BAM file
bam samtools RNA-Seq
updated 7.1 years ago by 104k • written 7.1 years ago by ▴ 270
2
votes
1
reply
3.1k
views
Piping samtools merge to samtools calmd
samtools pipe
7.2 years ago by rubic ▴ 270
6
votes
7
replies
4.7k
views
Create a UCSC chain file from a VCF
genome vcf chain
updated 7.3 years ago by ★ 1.5k • written 10.1 years ago by ▴ 270
2
votes
1
reply
3.4k
views
Parsing BLAST pairwise output in R
R blast parse
7.3 years ago by rubic ▴ 270
0
votes
1
reply
1.7k
views
Pruning a reference phylogenetic tree according to input species
phylogenetics taxonomy
updated 7.4 years ago by ★ 3.0k • written 7.6 years ago by ▴ 270
9
votes
7
replies
7.0k
views
Count and location of strings in fastq file reads
RNA-Seq kmer suffix tree
updated 7.4 years ago by 11k • written 7.8 years ago by ▴ 270
0
votes
1
reply
1.6k
views
Finding clusters of interacting proteins in a protein-protein interaction graph
ppi graph protein-protein-interaction enrichment
updated 7.4 years ago by ▴ 650 • written 7.4 years ago by ▴ 270
6
votes
2
replies
4.0k
views
Piping a bam file to samtools calmd
samtools calmd pipe
updated 7.4 years ago by 7.4k • written 7.4 years ago by ▴ 270
2
votes
0
replies
2.3k
views
Producing transcriptomic bam with STAR with all sam attributes
RNA-Seq STAR
updated 7.4 years ago by 12k • written 7.4 years ago by ▴ 270
1
vote
1
reply
3.9k
views
Annotating gene clusters in a heatmap with GO enriched terms
RNA-Seq GO heatmap
updated 7.5 years ago by • 0 • written 7.5 years ago by ▴ 270
14
votes
6
replies
29k
views
GO enrichment analysis using R
GO GO-slim enrichment-analysis R
updated 7.5 years ago by ★ 2.6k • written 7.5 years ago by ▴ 270
2
votes
4
replies
3.4k
views
Empty output from Picard's EstimateLibraryComplexity
RNA-Seq picard EstimateLibraryComplexity
7.7 years ago by rubic ▴ 270
9
votes
12
replies
12k
views
Efficiently extract alignments with NH:i:1 field
alignment RNA-Seq
updated 17 months ago by 44k • written 8.9 years ago by ▴ 270
1
vote
2
replies
2.1k
views
Counting ambiguously mapped reads per feature
RNA-Seq gtf bam count
updated 7.7 years ago by 20 • written 7.8 years ago by ▴ 270
3
votes
13
replies
3.9k
views
Converting to fastq and demultiplexing Illumina Hiseq4000 data using bcl2fastq
RNA-Seq bcl2fastq illumina hiseq4000
7.8 years ago by rubic ▴ 270
0
votes
1
reply
2.0k
views
At figure for an enrichment analysis
gsea plot metabolomics enrichment
updated 8.0 years ago by 7.5k • written 8.0 years ago by ▴ 270
1
vote
1
reply
3.5k
views
Getting the GT field from a vcf for all samples for a selected list of positions
vcf
8.2 years ago by rubic ▴ 270
1
vote
0
replies
2.3k
views
Phasing X chromosome variants using shapeit2
SNP next-gen-sequencing
updated 22 months ago by 44k • written 8.3 years ago by ▴ 270
1
vote
1
reply
4.9k
views
Badly formed genome loc: Contig '20' does not match any contig in the GATK sequence dictionary derived from the reference
gatk RNA-Seq
updated 2.1 years ago by 44k • written 8.4 years ago by ▴ 270
0
votes
1
reply
4.7k
views
Getting: Error reading _plen[] array: 1776466139, 4294967292 with TopHat2/bowtie2
bowtie tophat RNA-Seq
updated 24 months ago by 44k • written 9.2 years ago by ▴ 270
2
votes
4
replies
2.5k
views
RNA-seq stranded protocol
RNA-Seq
updated 2.6 years ago by 44k • written 9.9 years ago by ▴ 270
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