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353 results • Page
1 of 8
Sort: replies
Rank
Views
Votes
Replies
1
vote
13
replies
966
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 3 days ago by
lcj34
▴ 410 • written 9 days ago by
b.contreras.moreira
▴ 70
0
votes
12
replies
569
views
BWA MEM different synthax on linux (bash) and macOS (zsh)
MEM
BWA
21 days ago by
gernophil
▴ 80
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 2 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
1
vote
12
replies
546
views
Nanopore data filtering using fastp
fastp
nanopore
17 hours ago by
emilydolivo97
• 0
0
votes
11
replies
675
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 12 days ago by
barslmn
★ 2.1k • written 23 days ago by
avelarbio46
▴ 30
1
vote
11
replies
307
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 15 hours ago by
GenoMax
140k • written 21 hours ago by
Lila M
★ 1.2k
2
votes
10
replies
727
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 18 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
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
0
votes
9
replies
282
views
Low number of both surviving reads after trimming
trimmomatic
trimming
9 hours ago by
Jay
• 0
0
votes
9
replies
461
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 20 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
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
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
441
views
miRNA alignment with Bowtie2
bowtie2
13 days ago by
Chironex
▴ 40
0
votes
8
replies
419
views
STAR aligner options
STAR
22 hours ago by
theophile
• 0
2
votes
8
replies
263
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
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
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
0
votes
7
replies
323
views
single nuclei sequencing questions
fastq
single-nuclei-sequencing
updated 20 days ago by
Ram
43k • written 21 days ago by
Long
• 0
1
vote
7
replies
436
views
limma eBayes error in analysis of Illumina HumanHT-12 V4.0 expression beadchip data
R
beadchip
limma
microarray
Illumina
updated 29 days ago by
1769mkc
★ 1.2k • written 29 days ago by
accibio
▴ 20
1
vote
7
replies
831
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 2 days ago by
Ram
43k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
2
votes
7
replies
506
views
Need a link to OLDERADO server
pdb
protein
nmr
structure
16 days ago by
b2003
• 0
3
votes
7
replies
427
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
22 days ago by
Fadlilah
▴ 10
0
votes
7
replies
322
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 1 day ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
7
replies
441
views
Using VEP annotation output as the input for a second VEP annotation
VCF
VEP
Annotation
updated 16 days ago by
Ram
43k • written 8 weeks ago by
Arton
• 0
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 4 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
0
votes
7
replies
389
views
Error "ckalloc: request for negative space" about multiz
multiz
24 days ago by
marh32
• 0
0
votes
6
replies
369
views
why the file is low after combining the Hi-C reads using Arima genomics pipeline of mapping
bwa
mapping
genome
samtools
plants
20 days ago by
rj.rezwan
• 0
0
votes
6
replies
407
views
Download Panther entry list
PANTHER
7 days ago by
Nicolas
• 0
1
vote
6
replies
1.2k
views
Plots coloring in BPGA pan genome analysis pipeline
genome
next-gen
pan-genome
27 days ago by
hafiz.talhamalik
▴ 350
2
votes
6
replies
462
views
single cell RNA seq integration(Error in UseMethod(generic = "as.sparse", object = x))
scRNA-seq
20 days ago by
kayah
• 0
0
votes
6
replies
488
views
Rooting phylogenetic trees in R using Treeio's root function: Trees don't seem to root.
R
MrBayes
22 days ago by
lingxue
• 0
0
votes
6
replies
367
views
Contamination in my FASTQC files
Fastqc
bowtie2
20 days ago by
carlosgonzalezcruz327
▴ 20
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
6 days ago by
tujuchuanli
▴ 100
2
votes
6
replies
453
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
4
votes
6
replies
291
views
Protein loops
protein
Loop
14 days ago by
Curious
▴ 10
1
vote
5
replies
347
views
How to normalise RNA seq data from two independent experiments to the same scale.
RNAseq
updated 22 days ago by
jv
★ 1.7k • written 23 days ago by
Mo
▴ 40
1
vote
5
replies
375
views
Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?
sraexplorer
sratoolkit
updated 17 days ago by
GenoMax
140k • written 20 days ago by
biotrekker
▴ 100
0
votes
5
replies
407
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
6 days ago by
Learner
• 0
1
vote
5
replies
257
views
how to convert SummarizedExperiment files to DESeqDataSet??
scRNA-seq
DEG
DESeq2
updated 16 days ago by
Haci
▴ 550 • written 16 days ago by
kayah
• 0
0
votes
5
replies
291
views
Bedtools getfasta: error
getfasta
bedtools
updated 17 days ago by
GenoMax
140k • written 17 days ago by
ummeswaiba
• 0
0
votes
5
replies
392
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
16 days ago by
Maxwell
▴ 20
0
votes
5
replies
317
views
Parsing fasta file by coordinates
linux
fasta
updated 15 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
0
votes
5
replies
351
views
loop string set
python
stringset
updated 23 days ago by
rpolicastro
13k • written 24 days ago by
aj123
▴ 120
2
votes
5
replies
2.3k
views
GTF file for HIV strain pNL4-3
HIV
annotation
mapping
updated 28 days ago by
xiaoleiusc
▴ 140 • written 5.8 years ago by
caggtaagtat
★ 1.8k
2
votes
5
replies
608
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 14 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
K
• 0
1
vote
5
replies
410
views
Haddock 2.4
Protein
Docking
updated 8 days ago by
dthorbur
★ 1.7k • written 10 days ago by
Preeti
• 0
1
vote
5
replies
267
views
Merging bam files from different runs
samtools
bam
updated 17 days ago by
GenoMax
140k • written 17 days ago by
shpak.max
▴ 50
0
votes
5
replies
363
views
Issues with bcftools
Bcftools
updated 21 days ago by
Pierre Lindenbaum
160k • written 22 days ago by
hgrsce
• 0
0
votes
4
replies
244
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
20 hours ago by
rohitsatyam102
▴ 840
1
vote
4
replies
302
views
Differential analysis using R
DNA
methylation
updated 23 days ago by
Michael
54k • written 24 days ago by
maryak
▴ 20
353 results • Page
1 of 8
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…
Comment: vcf file: number of samples does not match number of columns
by
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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