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386
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Handling NA values in limma's voom design matrix
rna-seq voom design.matrix limma NA
updated 8 months ago by 68k • written 8 months ago by ▴ 260
0
votes
1
reply
247
views
Extract primary STAR mapped reads to specific chromosomes
samtools STAR
updated 12 months ago by ★ 1.2k • written 12 months ago by ▴ 260
1
vote
1
reply
384
views
Quantifying expression levels of IsoSeq reads with Kallisto
IsoSeq Kallisto expression
updated 12 months ago by ★ 3.7k • written 12 months ago by ▴ 260
0
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0
replies
741
views
Comment: Comment: Distinguishing between ambiguously mapped reads in a split bamToBed file
13 months ago by rubic ▴ 260
1
vote
2
replies
741
views
Distinguishing between ambiguously mapped reads in a split bamToBed file
reads RNA-Seq bam bamToBed split
13 months ago by rubic ▴ 260
2
votes
1
reply
326
views
Extract the mapped portion of the read sequence
bam RNA-Seq cigar
updated 13 months ago by 68k • written 13 months ago by ▴ 260
2
votes
1
reply
344
views
Usage of bedTools
bedTools bamToBed
13 months ago by rubic ▴ 260
0
votes
0
replies
260
views
Extract overlapping sequences from a bam file
bam RNA-Seq split splicing cigar
13 months ago by rubic ▴ 260
1
vote
1
reply
449
views
Downloading the IMGT/V-QUEST software
vquest software
updated 5 days ago by ▴ 990 • written 14 months ago by ▴ 260
1
vote
0
replies
286
views
Biostrings readDNAStringSet handling of N bases
Biostrings
16 months ago by rubic ▴ 260
0
votes
0
replies
485
views
HLA haplotypes VCF
HLA Haplotype VCF
18 months ago by rubic ▴ 260
0
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1
reply
1.3k
views
Comment: Comment: Fast parsing genbank files
22 months ago by rubic ▴ 260
0
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1
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1.3k
views
Comment: Comment: Fast parsing genbank files
22 months ago by rubic ▴ 260
3
votes
5
replies
1.3k
views
Fast parsing genbank files
Genbank parsing R
updated 22 months ago by 96k • written 22 months ago by ▴ 260
0
votes
1
reply
669
views
Blast a CDD PSSM against a genome
pssm CDD blast
updated 22 months ago by ★ 22k • written 22 months ago by ▴ 260
0
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1
reply
791
views
Comment: Comment: Searching for conserved domains in a chromosome/scaffold
22 months ago by rubic ▴ 260
1
vote
3
replies
791
views
Searching for conserved domains in a chromosome/scaffold
blast domain CDD PSSM rpsblast
updated 22 months ago by ★ 22k • written 22 months ago by ▴ 260
1
vote
1
reply
757
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 2.0 years ago by 152k • written 2.0 years ago by ▴ 260
2
votes
1
reply
894
views
GET Ensembl xrefs for multiple queries
ensembl httr api
updated 2.5 years ago by ★ 2.1k • written 2.5 years ago by ▴ 260
1
vote
0
replies
4.0k
views
Answer: A: Create a UCSC chain file from a VCF
updated 3.1 years ago by 37k • written 8.8 years ago by ▴ 260
0
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1
reply
4.0k
views
Comment: C: Create a UCSC chain file from a VCF
updated 3.1 years ago by 37k • written 8.8 years ago by ▴ 260
1
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0
replies
10k
views
Comment: C: Efficiently extract alignments with NH:i:1 field
updated 3.2 years ago by 37k • written 7.6 years ago by ▴ 260
0
votes
1
reply
984
views
Comment: C: Get Ensembl mapping between the chromosome and scaffold names
3.6 years ago by rubic ▴ 260
0
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0
replies
984
views
Comment: C: Get Ensembl mapping between the chromosome and scaffold names
3.6 years ago by rubic ▴ 260
3
votes
5
replies
984
views
Get Ensembl mapping between the chromosome and scaffold names
ensembl Assembly scaffold chromosome
updated 3.6 years ago by ▴ 290 • written 3.6 years ago by ▴ 260
0
votes
0
replies
1.2k
views
Comment: C: AGP files in Ensembl
3.8 years ago by rubic ▴ 260
1
vote
4
replies
1.2k
views
AGP files in Ensembl
Assembly AGP ensembl
updated 3.8 years ago by 23k • written 3.8 years ago by ▴ 260
0
votes
1
reply
840
views
Parse sim4 output alignment format
sim4 pairwise alignment parse
4.0 years ago by rubic ▴ 260
2
votes
2
replies
1.5k
views
Error while building picard tools from broadinstitute-picard-a4d54b4
picard broad
updated 4.4 years ago by 37k • written 7.0 years ago by ▴ 260
0
votes
1
reply
1.1k
views
Getting transcriptomic coordinates for CDS exons from a GTF
GTF BED
4.8 years ago by rubic ▴ 260
0
votes
0
replies
1.3k
views
Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
4.8 years ago by rubic ▴ 260
0
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1
reply
1.3k
views
Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
4.8 years ago by rubic ▴ 260
1
vote
4
replies
1.3k
views
Running salmon after subsetting the bam to transcripts annotated as protein coding in the GTF
salmon samtools GTF gencode
4.8 years ago by rubic ▴ 260
1
vote
1
reply
1.5k
views
Does samtools view -b -h <input.bam> -L <input.bed> keep the original header?
samtools header
updated 4.8 years ago by ★ 2.8k • written 4.8 years ago by ▴ 260
0
votes
1
reply
945
views
Number of sequenced positions from a BAM file
bam samtools RNA-Seq
updated 5.8 years ago by 102k • written 5.8 years ago by ▴ 260
2
votes
1
reply
2.6k
views
Piping samtools merge to samtools calmd
samtools pipe
5.9 years ago by rubic ▴ 260
6
votes
7
replies
4.0k
views
Create a UCSC chain file from a VCF
genome vcf chain
updated 6.0 years ago by ★ 1.3k • written 8.8 years ago by ▴ 260
2
votes
1
reply
3.0k
views
Parsing BLAST pairwise output in R
R blast parse
6.0 years ago by rubic ▴ 260
0
votes
1
reply
1.5k
views
Pruning a reference phylogenetic tree according to input species
phylogenetics taxonomy
updated 6.0 years ago by ★ 3.0k • written 6.3 years ago by ▴ 260
9
votes
7
replies
5.6k
views
Count and location of strings in fastq file reads
RNA-Seq kmer suffix tree
updated 6.1 years ago by 11k • written 6.5 years ago by ▴ 260
0
votes
1
reply
1.3k
views
Finding clusters of interacting proteins in a protein-protein interaction graph
ppi graph protein-protein-interaction enrichment
updated 6.1 years ago by ▴ 640 • written 6.1 years ago by ▴ 260
5
votes
2
replies
3.5k
views
Piping a bam file to samtools calmd
samtools calmd pipe
updated 6.1 years ago by 7.4k • written 6.1 years ago by ▴ 260
2
votes
0
replies
2.0k
views
Producing transcriptomic bam with STAR with all sam attributes
RNA-Seq STAR
updated 6.1 years ago by 12k • written 6.1 years ago by ▴ 260
1
vote
1
reply
3.7k
views
Annotating gene clusters in a heatmap with GO enriched terms
RNA-Seq GO heatmap
updated 6.2 years ago by • 0 • written 6.2 years ago by ▴ 260
0
votes
1
reply
25k
views
Comment: C: GO enrichment analysis using R
6.2 years ago by rubic ▴ 260
14
votes
6
replies
25k
views
GO enrichment analysis using R
GO GO-slim enrichment-analysis R
updated 6.2 years ago by ★ 2.6k • written 6.2 years ago by ▴ 260
2
votes
0
replies
25k
views
Comment: C: GO enrichment analysis using R
6.2 years ago by rubic ▴ 260
0
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1
reply
3.0k
views
Comment: C: Empty output from Picard's EstimateLibraryComplexity
6.3 years ago by rubic ▴ 260
2
votes
4
replies
3.0k
views
Empty output from Picard's EstimateLibraryComplexity
RNA-Seq picard EstimateLibraryComplexity
6.3 years ago by rubic ▴ 260
8
votes
12
replies
10k
views
Efficiently extract alignments with NH:i:1 field
alignment RNA-Seq
updated 6 weeks ago by 37k • written 7.6 years ago by ▴ 260
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