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Comment: Comment: Computing pairwise AA global sequence alignment between all pairs in a vector of
2.2 years ago by rubic ▴ 270
0
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1
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1.4k
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Comment: Comment: Computing pairwise AA global sequence alignment between all pairs in a vector of
2.2 years ago by rubic ▴ 270
2
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4
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1.4k
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Computing pairwise AA global sequence alignment between all pairs in a vector of sequences
pairwiseAlignment
2.2 years ago by rubic ▴ 270
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0
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1.1k
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Comment: Comment: Gene set enrichment analysis for genetic interactions
2.5 years ago by rubic ▴ 270
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0
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1.1k
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Comment: Comment: Gene set enrichment analysis for genetic interactions
2.6 years ago by rubic ▴ 270
1
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3
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1.1k
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Gene set enrichment analysis for genetic interactions
gsea genetic-interactions
2.5 years ago by rubic ▴ 270
1
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1
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1.4k
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Handling NA values in limma's voom design matrix
rna-seq voom design.matrix limma NA
updated 3.5 years ago by 90k • written 3.5 years ago by ▴ 270
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1
reply
727
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Extract primary STAR mapped reads to specific chromosomes
samtools STAR
updated 3.8 years ago by ★ 1.7k • written 3.8 years ago by ▴ 270
1
vote
1
reply
942
views
Quantifying expression levels of IsoSeq reads with Kallisto
IsoSeq Kallisto expression
updated 3.8 years ago by ★ 7.8k • written 3.8 years ago by ▴ 270
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0
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1.5k
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Comment: Comment: Distinguishing between ambiguously mapped reads in a split bamToBed file
3.9 years ago by rubic ▴ 270
1
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2
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1.5k
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Distinguishing between ambiguously mapped reads in a split bamToBed file
reads RNA-Seq bam bamToBed split
3.9 years ago by rubic ▴ 270
2
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1
reply
807
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Extract the mapped portion of the read sequence
bam RNA-Seq cigar
updated 3.9 years ago by 90k • written 3.9 years ago by ▴ 270
2
votes
1
reply
983
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Usage of bedTools
bedTools bamToBed
3.9 years ago by rubic ▴ 270
0
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0
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674
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Extract overlapping sequences from a bam file
bam RNA-Seq split splicing cigar
3.9 years ago by rubic ▴ 270
1
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1
reply
1.2k
views
Downloading the IMGT/V-QUEST software
vquest software
updated 2.8 years ago by ★ 1.0k • written 4.0 years ago by ▴ 270
1
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0
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805
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Biostrings readDNAStringSet handling of N bases
Biostrings
4.1 years ago by rubic ▴ 270
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0
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1.2k
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HLA haplotypes VCF
HLA Haplotype VCF
4.3 years ago by rubic ▴ 270
0
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1
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3.2k
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Comment: Comment: Fast parsing genbank files
4.6 years ago by rubic ▴ 270
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1
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3.2k
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Comment: Comment: Fast parsing genbank files
4.6 years ago by rubic ▴ 270
3
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5
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3.2k
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Fast parsing genbank files
Genbank parsing R
updated 4.6 years ago by 103k • written 4.6 years ago by ▴ 270
0
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1
reply
1.4k
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Blast a CDD PSSM against a genome
pssm CDD blast
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 270
0
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1
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2.2k
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Comment: Comment: Searching for conserved domains in a chromosome/scaffold
4.6 years ago by rubic ▴ 270
1
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3
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2.2k
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Searching for conserved domains in a chromosome/scaffold
blast domain CDD PSSM rpsblast
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 270
1
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1
reply
1.3k
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 4.8 years ago by 166k • written 4.8 years ago by ▴ 270
2
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1
reply
1.9k
views
GET Ensembl xrefs for multiple queries
ensembl httr api
updated 5.2 years ago by ★ 2.4k • written 5.2 years ago by ▴ 270
1
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0
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5.7k
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Answer: A: Create a UCSC chain file from a VCF
updated 5.9 years ago by 45k • written 11.6 years ago by ▴ 270
0
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1
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5.7k
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Comment: C: Create a UCSC chain file from a VCF
updated 5.9 years ago by 45k • written 11.6 years ago by ▴ 270
1
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0
replies
14k
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Comment: C: Efficiently extract alignments with NH:i:1 field
updated 6.0 years ago by 45k • written 10.4 years ago by ▴ 270
0
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1
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2.7k
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Comment: C: Get Ensembl mapping between the chromosome and scaffold names
6.4 years ago by rubic ▴ 270
0
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0
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2.7k
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Comment: C: Get Ensembl mapping between the chromosome and scaffold names
6.4 years ago by rubic ▴ 270
3
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5
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2.7k
views
Get Ensembl mapping between the chromosome and scaffold names
ensembl Assembly scaffold chromosome
updated 6.4 years ago by ▴ 290 • written 6.4 years ago by ▴ 270
0
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0
replies
2.1k
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Comment: C: AGP files in Ensembl
6.5 years ago by rubic ▴ 270
1
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4
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2.1k
views
AGP files in Ensembl
Assembly AGP ensembl
updated 6.5 years ago by 24k • written 6.6 years ago by ▴ 270
0
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1
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1.3k
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Parse sim4 output alignment format
sim4 pairwise alignment parse
6.7 years ago by rubic ▴ 270
2
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2
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2.0k
views
Error while building picard tools from broadinstitute-picard-a4d54b4
picard broad
updated 7.1 years ago by 45k • written 9.7 years ago by ▴ 270
0
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1
reply
1.7k
views
Getting transcriptomic coordinates for CDS exons from a GTF
GTF BED
7.6 years ago by rubic ▴ 270
0
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0
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2.2k
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Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
7.6 years ago by rubic ▴ 270
0
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1
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2.2k
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Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
7.6 years ago by rubic ▴ 270
1
vote
4
replies
2.2k
views
Running salmon after subsetting the bam to transcripts annotated as protein coding in the GTF
salmon samtools GTF gencode
7.6 years ago by rubic ▴ 270
1
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1
reply
2.3k
views
Does samtools view -b -h <input.bam> -L <input.bed> keep the original header?
samtools header
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 270
0
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1
reply
1.3k
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Number of sequenced positions from a BAM file
bam samtools RNA-Seq
updated 8.6 years ago by 105k • written 8.6 years ago by ▴ 270
2
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1
reply
3.5k
views
Piping samtools merge to samtools calmd
samtools pipe
8.7 years ago by rubic ▴ 270
6
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7
replies
5.7k
views
Create a UCSC chain file from a VCF
genome vcf chain
updated 8.8 years ago by ★ 1.5k • written 11.6 years ago by ▴ 270
2
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1
reply
3.8k
views
Parsing BLAST pairwise output in R
R blast parse
8.8 years ago by rubic ▴ 270
0
votes
1
reply
2.0k
views
Pruning a reference phylogenetic tree according to input species
phylogenetics taxonomy
updated 8.8 years ago by ★ 3.0k • written 9.0 years ago by ▴ 270
9
votes
7
replies
8.2k
views
Count and location of strings in fastq file reads
RNA-Seq kmer suffix tree
updated 8.9 years ago by 11k • written 9.3 years ago by ▴ 270
0
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1
reply
1.9k
views
Finding clusters of interacting proteins in a protein-protein interaction graph
ppi graph protein-protein-interaction enrichment
updated 8.9 years ago by ▴ 650 • written 8.9 years ago by ▴ 270
6
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2
replies
4.6k
views
Piping a bam file to samtools calmd
samtools calmd pipe
updated 8.9 years ago by 7.4k • written 8.9 years ago by ▴ 270
2
votes
0
replies
2.6k
views
Producing transcriptomic bam with STAR with all sam attributes
RNA-Seq STAR
updated 8.9 years ago by 12k • written 8.9 years ago by ▴ 270
1
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1
reply
4.3k
views
Annotating gene clusters in a heatmap with GO enriched terms
RNA-Seq GO heatmap
updated 8.9 years ago by • 0 • written 8.9 years ago by ▴ 270
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