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questions
2
votes
3
replies
371
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 19 days ago by
Michael
54k • written 19 days ago by
LDT
▴ 340
1
vote
2
replies
945
views
How to Modify Reference Sequence and Annotation Files
reference
edit
annotation
updated 7 weeks ago by
yeastbuddy
• 0 • written 2.1 years ago by
LDT
▴ 340
11
votes
3
replies
870
views
Whole genome comparison of two closely related plant species
mummer
comparative-genomics
whole-genome-alignment
whole-genome-comparison
mauve
updated 12 months ago by
SanjidaR_NCBI
▴ 60 • written 13 months ago by
LDT
▴ 340
5
votes
9
replies
3.8k
views
Transform a data.frame to GRranges in R
GenomicRanges
R
data.frame
bed
updated 17 months ago by
Mannu
• 0 • written 21 months ago by
LDT
▴ 340
6
votes
8
replies
1.3k
views
Understanding 1/1 output in VCF
vcf
17 months ago by
LDT
▴ 340
5
votes
7
replies
1.1k
views
How to find newly submitted accessions in NCBI
ncbi
updated 12 months ago by
corrector
▴ 30 • written 17 months ago by
LDT
▴ 340
2
votes
1
reply
878
views
Convert a bed file to bigbed
bed
bed12
ucsc
updated 17 months ago by
Matthias Zepper
4.6k • written 17 months ago by
LDT
▴ 340
7
votes
1
reply
3.0k
views
Remove multiple samples from a VCF file using bcftools
vcf
bcftools
vcftools
updated 17 months ago by
Pierre Lindenbaum
161k • written 17 months ago by
LDT
▴ 340
5
votes
6
replies
934
views
error: Couldn't open trackDb.txt in hubCheck
UCSC
hubCheck
updated 17 months ago by
seidel
11k • written 17 months ago by
LDT
▴ 340
4
votes
2
replies
608
views
Convert gff to bed, including non coding elements
bed
RNA
non-coding
gff
17 months ago by
LDT
▴ 340
4
votes
4
replies
943
views
Error while converting a bed to bigBed file
bed
UCSC
kentUtils
bigBed
17 months ago by
LDT
▴ 340
1
vote
2
replies
1.3k
views
How to measure pairwise genetic distance in all samples of a VCF file
pop-gen
pairwise-distance
VCF
updated 18 months ago by
chrchang523
10k • written 18 months ago by
LDT
▴ 340
1
vote
1
reply
605
views
Calculate missing genotypes per sample with plink2
missing
vcf
plink2
genotypes
updated 18 months ago by
chrchang523
10k • written 18 months ago by
LDT
▴ 340
1
vote
4
replies
1.1k
views
How to convert transcript counts to gene counts
tximport
r
gene_counts
RNAseq
updated 18 months ago by
manaswwm
▴ 510 • written 18 months ago by
LDT
▴ 340
3
votes
5
replies
2.1k
views
Count missing and non missing values in a VCF file
vcf
bcftools
vcftools
updated 18 months ago by
raphael.B
▴ 520 • written 18 months ago by
LDT
▴ 340
8
votes
8
replies
888
views
How to convert heterozygous variants to ./. in a VCF file?
heterozygosity
vcf
bcftools
updated 19 months ago by
Ram
43k • written 19 months ago by
LDT
▴ 340
7
votes
6
replies
1.3k
views
How to convert a for loop to a Job-array in LSF cluster
lsf
cluster-computing
Job-array
hpc
updated 19 months ago by
5heikki
11k • written 19 months ago by
LDT
▴ 340
1
vote
2
replies
567
views
Can you use kallisto to process GRO-seq data?
pNet-seq
GRO-seq
kallisto
19 months ago by
LDT
▴ 340
7
votes
9
replies
1.7k
views
Is it possible to run MultiQC on different batches of files?
fastQC
multiQC
updated 6 months ago by
Oliver
▴ 10 • written 20 months ago by
LDT
▴ 340
3
votes
1
reply
516
views
Change ReadGroup name with BWA mem in a group of paired-end files
bam
bwa
bwa-mem
updated 20 months ago by
Istvan Albert
100k • written 20 months ago by
LDT
▴ 340
4
votes
2
replies
528
views
How to normalise counts to compare RNAseq results between two spcecies
DESeq2
RNAseq
normalisation
updated 15 months ago by
Lada
▴ 30 • written 20 months ago by
LDT
▴ 340
0
votes
1
reply
434
views
Do you need to sort bam files that you have intersected before with bedtools
bedtools
bam
updated 10 months ago by
Ram
43k • written 20 months ago by
LDT
▴ 340
1
vote
0
replies
382
views
Correlation Plot of Two Biological Replicates of GRO-seq Data
groHMM
GRO-seq
HOMER
21 months ago by
LDT
▴ 340
2
votes
1
reply
2.3k
views
Convert an R data.frame to a bed file in R
bam
bed
bedtools
R
rtracklayer
updated 21 months ago by
rpolicastro
13k • written 21 months ago by
LDT
▴ 340
4
votes
3
replies
858
views
How to remove Illumina Small RNA 3' Adapter?
cutadapt
trimm
trimmomatic
updated 22 months ago by
GenoMax
142k • written 22 months ago by
LDT
▴ 340
1
vote
3
replies
1.1k
views
How to remove polyAAA tails with Trimmomatic
polyAAA
trimming
trimmomatic
updated 22 months ago by
GenoMax
142k • written 22 months ago by
LDT
▴ 340
1
vote
1
reply
414
views
blastn a query to a masked subject
refrence
masked
reference
align
blastn
updated 2.1 years ago by
lieven.sterck
15k • written 2.1 years ago by
LDT
▴ 340
9
votes
6
replies
2.4k
views
Extract from a .bam file the reads that map to specific area in the reference genome
alignment
sequences
bam
extract
updated 21 months ago by
Prakki Rama
★ 2.7k • written 2.3 years ago by
LDT
▴ 340
3
votes
6
replies
1.2k
views
How can I extract part of the DNA sequences that align to a specific region in the reference from a .bam file?
bedtools
alignment
samtools
bam
sequences
2.2 years ago by
LDT
▴ 340
1
vote
1
reply
599
views
How to map amplicon sequences to a reference with masked sequences?
reference
amplicon
bwa
bowtie2
alignment
updated 12 months ago by
corrector
▴ 30 • written 2.4 years ago by
LDT
▴ 340
4
votes
2
replies
1.4k
views
Extract strings based on multiple patterns in R
DNA
strings
Biostrings
r
Levenhstein
updated 2.4 years ago by
cpad0112
21k • written 2.4 years ago by
LDT
▴ 340
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