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214 results • Page
1 of 5
Sort: replies
Rank
Views
Votes
Replies
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 4 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 21 hours ago by
Ram
40k • written 12.3 years ago by
Palu
▴ 250
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 5 days ago by
zx8754
11k • written 10.7 years ago by
henryvuong
▴ 810
18
votes
22
replies
8.0k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 21 hours ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
75
votes
18
replies
2.0k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 4 days ago by
Ram
40k • written 9 days ago by
Kenny
▴ 30
16
votes
16
replies
1.8k
views
Species identifcation using 16s rRNA
16srRNA
fasta
updated 2 days ago by
Ram
40k • written 2.6 years ago by
A_heath
▴ 140
36
votes
16
replies
28k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 3 days ago by
jkbonfield
★ 1.1k • written 4.6 years ago by
chparada
▴ 60
7
votes
15
replies
3.3k
views
Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index
next-gen
sequencing
updated 4 days ago by
Gabriel R.
★ 2.9k • written 3.3 years ago by
Rezenman
• 0
19
votes
14
replies
793
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 2 days ago by
Jeremy Leipzig
21k • written 3 days ago by
vincenthus
▴ 70
0
votes
13
replies
461
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
1 hour ago by
Y
• 0
2
votes
13
replies
578
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn
Trinity
Transcriptome
RNA-seq-analysis
De-novo-transcriptome-assembly
1 day ago by
langziv
▴ 50
23
votes
12
replies
1.9k
views
Genes encoded on both strands of DNA?
Genes
strand
updated 2 days ago by
Ram
40k • written 16 months ago by
A_heath
▴ 140
9
votes
12
replies
4.2k
views
converting a list of genes and interaction to a graph
gene
R
updated 2 days ago by
Amirhossein Hajianpour
▴ 40 • written 7.7 years ago by
fi1d18
★ 4.2k
0
votes
11
replies
688
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
2 days ago by
evmae
• 0
8
votes
10
replies
672
views
Inflated GWAS test statistic after merging multiple batches of genotype dataset imputed differently
genotype
imputation
gwas
updated 2 days ago by
LauferVA
3.7k • written 4 days ago by
Amy
▴ 20
3
votes
10
replies
2.2k
views
Salmon alignment based quantification
Salmon
rna-seq
quantification
updated 1 day ago by
Mat
▴ 60 • written 18 months ago by
edus_bioinfo
▴ 40
1
vote
10
replies
872
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 10 hours ago by
jeffhsu3
• 0 • written 11 weeks ago by
fra.silvestro99
▴ 10
7
votes
10
replies
466
views
Batch effect normalization
RNA-seq
batch-effect
updated 4 days ago by
Ram
40k • written 5 days ago by
Smriti
• 0
3
votes
10
replies
433
views
STAR index not working
STAR
RNA-Seq
1 day ago by
camillab.
▴ 130
1
vote
9
replies
1.5k
views
Scanpy Pearson residual PCA error
python
scRNA
scanpy
PCA
updated 23 hours ago by
Ram
40k • written 13 months ago by
Emily
▴ 30
0
votes
8
replies
725
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
1 day ago by
pb11
▴ 10
5
votes
8
replies
5.3k
views
6 follow
How to repair corrupted fastq files after sortmeRNA
software error
RNA-Seq
alignment
updated 5 days ago by
Tommaso
• 0 • written 5.6 years ago by
SMILE
▴ 170
10
votes
8
replies
459
views
Adding a control sample to bulk RNA-seq
RNA-seq
1 day ago by
Chris
▴ 180
5
votes
8
replies
2.7k
views
Difference between total number of reads in fastq file and no of bases/nt sequences in fastq file?
FASTQ
updated 4 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
6
votes
8
replies
451
views
Find potential important genes from bulk-RNA seq experiment
RNA-seq
17 hours ago by
Chris
▴ 180
6
votes
7
replies
1.2k
views
wc -l or wc -c which linux command is best to find total read count in fastq file?
linux
updated 4 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
3
votes
7
replies
314
views
6 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 18 hours ago by
Ram
40k • written 1 day ago by
MVJ
• 0
2
votes
7
replies
1.4k
views
How to find newline character in fastq file? Is it essential to remove them?
FASTQ
updated 4 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
5
votes
7
replies
311
views
Salmon index not progressing
salmon
updated 22 hours ago by
Michael
53k • written 1 day ago by
camillab.
▴ 130
5
votes
7
replies
436
views
Elusive syntax error in Snakefile
snakemake
updated 3 days ago by
Ram
40k • written 4 days ago by
Giuseppe Giovanni
▴ 30
2
votes
7
replies
4.0k
views
GERP++ (gerpcol) error on a test data
GERP
updated 2 days ago by
Diana
• 0 • written 7.1 years ago by
kirill1984
▴ 10
0
votes
7
replies
779
views
Mugsy error -directory must be a directory
Mugsy
updated 2 days ago by
Ram
40k • written 2.8 years ago by
A_heath
▴ 140
0
votes
7
replies
1.5k
views
what does "total read count" means in fastqc file. how does it helpful for analysis
fastqc
updated 4 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
4
votes
7
replies
718
views
How to subtract a number from protein IDs?
blast
updated 2 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
7
votes
7
replies
3.8k
views
Genes with promoter and enhancer regions as GTF
ChIP-Seq
featurecounts
gtf
promoter
genes
updated 10 hours ago by
abis.1819104
• 0 • written 5.3 years ago by
hkarakurt
▴ 170
1
vote
6
replies
3.2k
views
Extracting sequence, not reads, by position from bam
sequence
updated 3 days ago by
manu
• 0 • written 5.0 years ago by
geneware
▴ 10
3
votes
6
replies
438
views
summarize consecutive columns over a data frame
tidyverse
r
offtopic
updated 21 hours ago by
Ram
40k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
6
replies
369
views
Read block operation failed with BAM file
bgzip
samtools
bam
pysam
htslib
4 days ago by
Alex Reynolds
35k
0
votes
6
replies
290
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
updated 2 hours ago by
4galaxy77
2.8k • written 1 day ago by
cwwong13
▴ 20
0
votes
6
replies
937
views
How to run delly with multi-threading mode?
SV
calling
delly
updated 3 days ago by
bio-jr
▴ 10 • written 8 months ago by
Xi
• 0
0
votes
6
replies
842
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
2 days ago by
ccbb7aab4
▴ 20
0
votes
6
replies
274
views
genome data downloads for various strains
gisaid
hass-marr
updated 1 day ago by
Ram
40k • written 2 days ago by
iftikharmaryam123
• 0
1
vote
5
replies
664
views
Mugsy percentage of identity
Mugsy
Genome-alignment
updated 2 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
8
votes
5
replies
359
views
Alphafold Cat
Joke
updated 3 days ago by
fishgolden
▴ 510 • written 11 days ago by
BioGrad321
• 0
8
votes
5
replies
1.6k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 2 days ago by
Ram
40k • written 23 months ago by
A_heath
▴ 140
3
votes
5
replies
379
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
updated 18 hours ago by
Mensur Dlakic
★ 24k • written 3 days ago by
Edoardo
• 0
0
votes
5
replies
321
views
manhattan plot with vcf information
R
manhattan
vcf
updated 2 days ago by
dthorbur
▴ 550 • written 4 days ago by
sooni
▴ 10
2
votes
5
replies
427
views
Uniprot Database for download
proteomics
Uniprot
updated 2 days ago by
Elisabeth Gasteiger
★ 2.3k • written 28 days ago by
SHN
▴ 40
2
votes
5
replies
220
views
Trimmomatic .jar not included anymore?
trimmomatic
ubuntu
linux
updated 1 day ago by
petebio
▴ 100 • written 1 day ago by
Emily
▴ 30
10
votes
5
replies
25k
views
FastQC with multiple FASTQ files
ngs
fastqc
multiple
updated 4 days ago by
Ram
40k • written 5.2 years ago by
m98
▴ 400
214 results • Page
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Comment: Hugo_Symbol to Entrez ID
by
GenoMax
134k
Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38
by
GenoMax
134k
GTF file includes gene models/annotation information. You could also use a program like `salmon/kallisto` with just human transcriptome to…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
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157k
then test each files. find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck file "${reference_gen…
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The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
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Y
• 0
I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended: # Run CuffDiff wit…
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157k
how about simply trying: ``` cuffdiff -u "${annotation_gtf}" \ -o "${output_directory}" \ -b "${reference_genome}" \ -p "${num_th…
Comment: Using STAR aligner to build index of hg38
by
Grace
• 0
Yes, I know also need a GTF file. So the GTF file will include RNA information? Thanks for your answer!!
Comment: STAR Intron Motif Script Gives Segmentation fault Error
by
Y
• 0
I will try and figure it out on my own given what you all have mentioned. Thank you for your time.
Comment: Using STAR aligner to build index of hg38
by
Amitm
★ 2.2k
Have you gone through the manual [here][1]. In addition to the genome fasta file, you would also need a GTF file (of gene annotations) to b…
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4galaxy77
2.8k
You still definitely need to include principle components as covariates, even if your data is from the same ethnicity. Not including those …
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Hi, D-genies is using minimap2 to align both genomes and minimap2 is chaining local alignments to produce a global one. If the SV are sm…
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In this case there are no results in my fgsea object unfortunately
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how to generate promoters.bed and enhancer.bed files from gtf file
Comment: Deepvariant variant calling by singularity
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jeffhsu3
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I am having a similar issue was this ever resolved? Getting this error: I0922 22:22:08.794076 140356687390528 make_examples_core.py:257] O…
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★ 24k
Probably there are people here for whom this is a trivial task, and maybe you will luck out and one of them will write a solution for you. …
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