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0
votes
1
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246
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 2 days ago by
GenoMax
141k • written 2 days ago by
predeus
★ 1.9k
2
votes
5
replies
601
views
API way to find "Original submitter" files in SRA?
fastq
SRA
8 weeks ago by
predeus
★ 1.9k
1
vote
7
replies
866
views
Samtools filtering based on PNEXT
CRAM
filtering
samtools
SAM
BAM
updated 5 months ago by
Istvan Albert
100k • written 5 months ago by
predeus
★ 1.9k
3
votes
1
reply
731
views
R package to link NCBI taxonomy ID to bacterial properties (Gram stain, aerobe/anaerobe, etc)
R
NCBI
bacteria
taxonomy
updated 8 months ago by
Philipp Bayer
8.3k • written 8 months ago by
predeus
★ 1.9k
1
vote
13
replies
1.5k
views
Merge BAM files from (totally) different references
bam
ngs
mapping
8 months ago by
predeus
★ 1.9k
2
votes
2
replies
410
views
Clustered bacterial RefSeq?
refseq
clustering
ANI
bacteria
8 months ago by
predeus
★ 1.9k
1
vote
3
replies
700
views
bbduk.sh trimmer with multiple input files
bbduk
bbmap
bbtools
updated 9 months ago by
GenoMax
141k • written 10 months ago by
predeus
★ 1.9k
3
votes
3
replies
1.2k
views
Read counting in RSEM and Salmon (alignment mode)
quantification
RSEM
RNA-seq
Salmon
12 months ago by
predeus
★ 1.9k
0
votes
0
replies
356
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
13 months ago by
predeus
★ 1.9k
6
votes
10
replies
1.5k
views
Automated way to pull representative/RefSeq genome using full species name?
ncbi
taxonomy
refseq
updated 16 months ago by
LChart
3.9k • written 16 months ago by
predeus
★ 1.9k
2
votes
3
replies
1.6k
views
bbduk paired-end RNA-seq trimming command
rna-seq
paired-end
bbduk
trimming
adapter
updated 20 months ago by
GenoMax
141k • written 20 months ago by
predeus
★ 1.9k
2
votes
4
replies
929
views
Specific case of "bedtools intersect"
bedtools
BAM
updated 10 months ago by
Ram
43k • written 2.0 years ago by
predeus
★ 1.9k
1
vote
3
replies
679
views
Sequence parsing question
seqtk
fastq
sequence
parsing
updated 2.1 years ago by
cpad0112
21k • written 2.1 years ago by
predeus
★ 1.9k
2
votes
3
replies
1.0k
views
Tools similar to entrez-direct for ENA?
SRA
Entrez-direct
ENA
Entrez
2.3 years ago by
predeus
★ 1.9k
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 15 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
4
votes
3
replies
1.2k
views
Cell cycle genes for D. melanogaster and C. elegans (for scRNA-seq analysis)
cycle-correction
single-cell
regression
scRNA-seq
bias
updated 2.6 years ago by
Friederike
8.9k • written 2.6 years ago by
predeus
★ 1.9k
1
vote
3
replies
1.2k
views
scRNAseq - infer type of single-cell chemistry from fastq
scRNA-seq
single cell
RNA-Seq
updated 2.6 years ago by
bosun1988
• 0 • written 3.2 years ago by
predeus
★ 1.9k
1
vote
2
replies
948
views
WGS bacterial metagenomic pipeline - group comparison
metagenomics
WGS
pipeline
bacterial
2.7 years ago by
predeus
★ 1.9k
5
votes
3
replies
4.5k
views
Kraken2 with Nanopore reads
kraken2
nanopore
kraken
2.8 years ago by
predeus
★ 1.9k
4
votes
9
replies
1.9k
views
Truncate unevenly covered BAM file at certain coverage
samtools
bam
2.9 years ago by
predeus
★ 1.9k
4
votes
5
replies
2.0k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq
scRNA-Seq
whole blood
single cell
11 months ago by
predeus
★ 1.9k
4
votes
5
replies
4.8k
views
Version history and design files for exome kits from Agilent, Roche(Nimblegen), and Illumina
exome
agilent
roche
nimblegen
illumina
updated 3.1 years ago by
jon.klonowski
▴ 150 • written 6.5 years ago by
predeus
★ 1.9k
1
vote
5
replies
1.1k
views
Cell type assignment for non-model organism single cell RNA-seq
RNA-Seq
scRNA-Seq
single cell
non-model organism
3.2 years ago by
predeus
★ 1.9k
3
votes
6
replies
1.8k
views
Get GEO microarray probe sequences by GPL ID
microarray
GEO
gene expression omnibus
3.9 years ago by
predeus
★ 1.9k
12
votes
4
replies
3.3k
views
16S-specific multiple alignment of rDNA sequences
multiple-sequence-alignment
16S
multiple-alignment
updated 11 months ago by
Ram
43k • written 4.0 years ago by
predeus
★ 1.9k
1
vote
3
replies
941
views
Genome-scale missense variant effect predictors?
provean
sift
polyphen
missense
sift4g
4.0 years ago by
predeus
★ 1.9k
1
vote
2
replies
771
views
Using MEME-suite to find sigma-factor binding sites (or other broad motifs)
meme
meme-chip
meme suite
motif
chip-seq
updated 4.1 years ago by
Asaf
10k • written 4.1 years ago by
predeus
★ 1.9k
2
votes
2
replies
841
views
A good tutorial for eukaryotic phylogeny?
phylogeny
tree
eukaryote
updated 4.3 years ago by
Vitis
★ 2.5k • written 4.4 years ago by
predeus
★ 1.9k
7
votes
5
replies
1.3k
views
Eukaryotic gene annotation on gene predictions
annotation
eukaryotic
gene prediction
updated 4.6 years ago by
Biostar
20 • written 4.7 years ago by
predeus
★ 1.9k
25
votes
25
replies
12k
views
11 follow
Modern software for whole genome alignment visualization
visualization
whole-genome alignment
mauve
harvest
updated 4.9 years ago by
gina
• 0 • written 6.1 years ago by
predeus
★ 1.9k
16
votes
7
replies
10k
views
Get a complete GSM-to-SRX/SRR table
GEO
SRA
GSM
GSE
SRAdb
updated 4.9 years ago by
Helen
▴ 50 • written 7.1 years ago by
predeus
★ 1.9k
12
votes
6
replies
8.7k
views
Racon-Illumina or Pilon?
Assembly
nanopore
polishing
updated 5.0 years ago by
sullis02
▴ 40 • written 5.9 years ago by
predeus
★ 1.9k
8
votes
6
replies
2.3k
views
Using Bandage to finish ambiguous long-read assembly?
Assembly
Bandage
long reads
Unicycler
updated 5.2 years ago by
Biostar
20 • written 5.3 years ago by
predeus
★ 1.9k
0
votes
2
replies
1.9k
views
Blocking primer design software?
blocking primers
PCR
amplification
updated 5.4 years ago by
lufiealf
• 0 • written 6.2 years ago by
predeus
★ 1.9k
1
vote
3
replies
995
views
Cluster plasmids of (very) different lengths
sequence clustering
blast
5.5 years ago by
predeus
★ 1.9k
5
votes
6
replies
3.4k
views
Best way to assign pfam/EC/COGs to a set of proteins
pfam
COG
enzyme
protein
5.5 years ago by
predeus
★ 1.9k
2
votes
4
replies
1.9k
views
Options for long-read diploid assembly
pacbio
nanopore
Assembly
diploid
updated 5.6 years ago by
harish
▴ 450 • written 5.6 years ago by
predeus
★ 1.9k
1
vote
1
reply
2.0k
views
Huge jump in plasmid coverage - any idea why?
bacteria
pacbio
pilon
illumina
6.1 years ago by
predeus
★ 1.9k
5
votes
7
replies
3.1k
views
Annotation with Prokka - small ORFs and genus-specific DB?
prokka
bacteria
annotation
updated 6.2 years ago by
Asaf
10k • written 6.2 years ago by
predeus
★ 1.9k
2
votes
4
replies
1.4k
views
How to change Bioperl's Bio::SeqIO default sequence folding?
bioperl
fasta
fastq
updated 6.6 years ago by
Chris Fields
★ 2.2k • written 6.6 years ago by
predeus
★ 1.9k
0
votes
0
replies
1.1k
views
Annotate multiple rRNAs with variable and constant regions
rRNA
multiple-alignment
SILVA
updated 11 months ago by
Ram
43k • written 6.8 years ago by
predeus
★ 1.9k
105
votes
81
replies
32k
views
17 follow
Duplicates on Illumina
duplicates
illumina
updated 19 months ago by
GenoMax
141k • written 7.3 years ago by
predeus
★ 1.9k
2
votes
1
reply
1.3k
views
Why do Drosophila genomes look haploid?
RNA-Seq
IGV
7.3 years ago by
predeus
★ 1.9k
6
votes
5
replies
2.9k
views
How can an assembled genome have Ns in it?
ngs
wgs
genome assembly
7.3 years ago by
predeus
★ 1.9k
2
votes
10
replies
1.5k
views
Finding foreign sequences in an NGS experiment
ngs
adapter
blastn
updated 7.4 years ago by
Farbod
★ 3.4k • written 7.4 years ago by
predeus
★ 1.9k
2
votes
4
replies
1.4k
views
List or wiki of major NGS-related consortia
RNA-Seq
ChIP-Seq
WES
WGS
updated 8.0 years ago by
Biostar
20 • written 8.0 years ago by
predeus
★ 1.9k
1
vote
4
replies
1.9k
views
Does any large resequencing project have a genuinely hg38 VCF?
exome
WGS
WES
resequencing
VCF
updated 8.0 years ago by
abascalfederico
★ 1.2k • written 8.0 years ago by
predeus
★ 1.9k
0
votes
2
replies
1.8k
views
PCA and DE analysis for loop design microarray
loop-design
Agilent
microarray
updated 19 months ago by
Ram
43k • written 8.6 years ago by
predeus
★ 1.9k
1
vote
3
replies
4.6k
views
Use esearch/efetch to output relationship table of GSM to SRR (bascially SRA file names)
GEO
GEO-omnibus
NCBI
9.9 years ago by
predeus
★ 1.9k
5
votes
2
replies
2.5k
views
Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
chip-seq
motif
10.0 years ago by
predeus
★ 1.9k
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