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833 results • Page
2 of 17
Sort: replies
Rank
Views
Votes
Replies
2
votes
10
replies
560
views
Can't properly use GATK Mutect2 to call somatic variants from my tumor/normal samples pair (BAM to VCF)
vaf
gatk
vcf
genomics
mutect2
updated 15 days ago by
GenoMax
140k • written 16 days ago by
Samuel
▴ 20
16
votes
10
replies
10k
views
8 follow
GRCh37.p13 download at NCBI FTP?
ncbi
reference
grch37
updated 19 days ago by
Sruthi
• 0 • written 5.5 years ago by
Marvin
▴ 220
4
votes
10
replies
619
views
PDB residue serial inconsistency and PDB id&UniProt ID mismatch
pdb
UniProtID
pdbID
updated 28 days ago by
Wayne
★ 1.9k • written 29 days ago by
Nafi
• 0
18
votes
10
replies
5.2k
views
Should I normalize read counts if I want to run plotPCA?
RNA-Seq
updated 20 days ago by
ella
• 0 • written 3.9 years ago by
c_u
▴ 520
2
votes
10
replies
724
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 15 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
3
votes
10
replies
570
views
Errors running PHG MakeInitialPHGDBPipelinePlugin (**UNASSIGNED**)
pangenome
plants
PHG
updated 14 days ago by
lcj34
▴ 410 • written 16 days ago by
b.contreras.moreira
▴ 70
3
votes
10
replies
656
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
6 days ago by
Lissa Cruz Saavedra
• 0
6
votes
10
replies
2.7k
views
How can Investigate if a Viral genome is circular or linear? And if it is single or double stranded?
Assembly
genome
updated 27 days ago by
Israel
• 0 • written 5.3 years ago by
GiV17
▴ 50
3
votes
10
replies
705
views
t-test in two groups, multiple rows
R
t-test
10 days ago by
sooni
▴ 20
15
votes
10
replies
7.5k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 1 day ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
0
votes
10
replies
781
views
Problem running scPred
scPred
scPredict
updated 15 days ago by
Ram
43k • written 12 weeks ago by
Nitin
• 0
1
vote
9
replies
441
views
miRNA alignment with Bowtie2
bowtie2
13 days ago by
Chironex
▴ 40
5
votes
9
replies
627
views
Porechop output?
porechop
Nanopore
updated 27 days ago by
GenoMax
140k • written 29 days ago by
giulia.trauzzi
▴ 10
4
votes
9
replies
502
views
Max length reads from fastq
fastq
updated 23 days ago by
Michael
54k • written 23 days ago by
marco.barr
▴ 30
0
votes
9
replies
460
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 18 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
4
votes
9
replies
1.4k
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
updated 22 days ago by
ATpoint
81k • written 10 months ago by
DanielEB_fisk
▴ 20
1
vote
9
replies
1.4k
views
blast retrieves "N/A" for taxonomic data
blast
blastn
updated 19 days ago by
flavianegrete
• 0 • written 3.3 years ago by
langziv
▴ 50
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 11 hours ago by
Ram
43k • written 17 months ago by
Manav
• 0
0
votes
9
replies
273
views
Low number of both surviving reads after trimming
trimmomatic
trimming
7 hours ago by
Jay
• 0
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
1 day ago by
Zeng Jingyu
▴ 60
4
votes
9
replies
670
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 3 days ago by
Simon
▴ 10 • written 7 days ago by
Maxwell
▴ 20
15
votes
9
replies
596
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 9 hours ago by
Dave Carlson
★ 1.7k • written 14 hours ago by
Ann
★ 2.4k
0
votes
9
replies
486
views
RNA_seq
RNA-seq
updated 14 days ago by
swbarnes2
14k • written 15 days ago by
daffodil
▴ 10
14
votes
9
replies
11k
views
8 follow
Downsample BAM file to specific amount of reads
bam
updated 13 days ago by
GenoMax
140k • written 2.6 years ago by
kstangline
▴ 80
5
votes
9
replies
3.7k
views
Can one plot % of variance using the plotMDS function?
limma
plotMDS
PCA
PCoA
% of varience
updated 27 days ago by
Gordon Smyth
★ 6.9k • written 3.8 years ago by
harelarik
▴ 90
4
votes
9
replies
893
views
Error in openning FastQC
fastqc
igv
updated 7 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
1
vote
9
replies
802
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 16 days ago by
Dave Carlson
★ 1.7k • written 17 days ago by
Matthew
• 0
0
votes
9
replies
452
views
Intersect genomic locations with genes
fanc
Chromatin
conformation
Hic
hic
updated 6 days ago by
zx8754
11k • written 6 days ago by
naveedhasan2000
• 0
3
votes
8
replies
6.2k
views
6 follow
Download CAZy database
genome
gene
database
cazy
updated 13 days ago by
GenoMax
140k • written 6.1 years ago by
anu014
▴ 190
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 2 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
1
vote
8
replies
683
views
6 follow
Using aspera-connect to UPLOAD fastq files to ENA on Linux
ENA
aspera-connect
ascp
updated 14 days ago by
jude
• 0 • written 15 days ago by
sue.jones
• 0
2
votes
8
replies
263
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
1
vote
8
replies
342
views
0-based coordinates from samtools depth
samtools
coverage
depth
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
marco.barr
▴ 30
11
votes
8
replies
5.0k
views
Multi-mapping High with featureCounts but not STAR
RNA-Seq
sequencing
alignment
updated 8 days ago by
GenoMax
140k • written 4.8 years ago by
garbuzov
▴ 70
2
votes
8
replies
440
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 8 days ago by
GenoMax
140k • written 10 days ago by
ben@f
▴ 10
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 14 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
0
votes
8
replies
1.4k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 14 days ago by
xiangbinruan
• 0 • written 18 months ago by
Phoebe Magdy
• 0
7
votes
8
replies
539
views
Forum:
Bioinformatics career transition
career
forum
updated 14 days ago by
jared.andrews07
★ 16k • written 14 days ago by
jevill17
▴ 20
5
votes
8
replies
515
views
Difference between GLM and Wilcoxon rank sum test
GLM
rank-sum
Wilcoxon
21 days ago by
yxwucq
• 0
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen
cutadapt
updated 14 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 20
4
votes
8
replies
469
views
i'm trying to use STAR and there is a problem...
STAR
updated 19 days ago by
GenoMax
140k • written 19 days ago by
markusz
▴ 10
0
votes
8
replies
510
views
Fine-tuning NCBI taxid / taxidlist
BLAST
taxonomy
7 days ago by
theclubstyle
▴ 40
17
votes
8
replies
5.0k
views
Mean Variance Relationship single cell RNA-Seq Data
RNA-Seq
variance
deseq2
single cell
updated 16 days ago by
thomas.heigl.ibk
• 0 • written 3.3 years ago by
kw486
▴ 30
0
votes
8
replies
419
views
STAR aligner options
STAR
20 hours ago by
theophile
• 0
2
votes
8
replies
1.2k
views
How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?
pymol
python
biopython
structural-bioinformatics
updated 23 days ago by
Wayne
★ 1.9k • written 5 weeks ago by
Aman Vishwakarma
• 0
7
votes
8
replies
409
views
Create Conda Environment with YAML File
Python
updated 13 days ago by
dthorbur
★ 1.7k • written 14 days ago by
cthangav
▴ 100
0
votes
7
replies
1.1k
views
Pan genome of genes
Get_homologues
updated 16 days ago by
b.contreras.moreira
▴ 70 • written 2.9 years ago by
Pedro
• 0
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 3 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
11
votes
7
replies
894
views
Shrink logFC values after edgeR
logFC
edgeR
updated 5 days ago by
Gordon Smyth
★ 6.9k • written 8 weeks ago by
arvind.1
▴ 10
2
votes
7
replies
525
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 15 days ago by
Chris Dean
▴ 390 • written 16 days ago by
ev97
▴ 20
833 results • Page
2 of 17
Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
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Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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