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1,000 results • Page 3 of 20
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3
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17
replies
987
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV DownSample fastq copy number not accurate
3.1 years ago by lffu_0032 ▴ 90
6
votes
17
replies
1.9k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen assembly genome alignment
4.8 years ago by williamsbrian5064 ▴ 470
0
votes
17
replies
2.2k
views
Fail running blastdb and blastn on my own computer
blast
5.4 years ago by annette440 • 0
27
votes
17
replies
16k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
15 months ago by Leite ★ 1.2k
3
votes
17
replies
2.3k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
24 months ago by boczniak767 ▴ 830
5
votes
17
replies
3.6k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics encode
9.0 years ago by 14134125465346445 ★ 3.6k
0
votes
17
replies
4.1k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 6 months ago by 38k • written 7.5 years ago by ▴ 30
1
vote
17
replies
1.8k
views
Snakemake Megahit error
megahit Snakemake
16 months ago by blackadder • 0
1
vote
17
replies
5.1k
views
BBMap: Mapping Fails
BBTools BBMap Mapping
updated 7.0 years ago by 127k • written 7.0 years ago by ▴ 50
2
votes
17
replies
5.9k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping genome fastq STAR
updated 12 months ago by • 0 • written 2.2 years ago by • 0
0
votes
17
replies
2.9k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq wgcna software error R next-gen
updated 15 months ago by • 0 • written 4.5 years ago by ▴ 20
4
votes
17
replies
2.1k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray gene-expression CV error
3.7 years ago by Jurat Shahidin ▴ 100
16
votes
17
replies
2.6k
views
6 follow
RNA seq pipeline
RNA-Seq
5.4 years ago by dimitrischat ▴ 180
2
votes
17
replies
4.4k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 5.0 years ago by 34k • written 5.0 years ago by ▴ 30
9
votes
17
replies
1.8k
views
Creating intergenic bam file
R genome intergenic alignment
6.6 years ago by erincyurtman • 0
7
votes
17
replies
5.9k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R gene genome
4.7 years ago by WUSCHEL ▴ 720
7
votes
17
replies
3.0k
views
How to find the differences in aligned bam files
RNA-Seq
6.1 years ago by krushnach80 ★ 1.1k
3
votes
17
replies
4.9k
views
Removing fastq duplicates
sequence next-gen ChIP-Seq
2.3 years ago by C4 ▴ 10
1
vote
17
replies
2.0k
views
Normalizing BLAST results
blast
updated 5.5 years ago by 20 • written 5.6 years ago by • 0
4
votes
17
replies
2.2k
views
Cufflinks analysis and gffread
RNA-Seq Assembly
updated 5.4 years ago by 84k • written 5.4 years ago by ▴ 100
2
votes
17
replies
3.9k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam bam alignment samtools
updated 9.2 years ago by 103k • written 9.2 years ago by ★ 1.5k
0
votes
17
replies
2.3k
views
I am not able to let R read my file
R fasta
updated 2.0 years ago by 3.1k • written 2.0 years ago by • 0
12
votes
17
replies
3.8k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python Newick phylogenetics tree phylogeny
5.4 years ago by anonymous1192976466 ▴ 50
7
votes
17
replies
3.6k
views
Strange MA-plot using DESeq2
rna-seq R deseq2
updated 6.2 years ago by 20 • written 6.3 years ago by ▴ 80
8
votes
17
replies
3.3k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
5.1 years ago by Sharon ▴ 580
1
vote
17
replies
3.3k
views
Error executing bedops convert2bed
bedops bed vcf convert2bed
6.2 years ago by lakhujanivijay 5.7k
7
votes
16
replies
2.9k
views
How do I get a GFF file
snp
3.7 years ago by apl00028 ▴ 70
0
votes
16
replies
3.9k
views
Issue using MaSuRCA-3.2.6
Assembly assembler
updated 4.6 years ago by 20 • written 4.8 years ago by ▴ 90
3
votes
16
replies
900
views
How to bring all reads to the same length? Any tool?
Read length Bed Tool
3.2 years ago by Ankit ▴ 390
9
votes
16
replies
888
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 2.6 years ago by 14k • written 2.6 years ago by ▴ 130
3
votes
16
replies
2.9k
views
GC content of 10x Genomics
fastqc 10x GC content
updated 2.6 years ago by ▴ 170 • written 4.0 years ago by ★ 1.8k
2
votes
16
replies
1.4k
views
I want to know is it a true method ?
vcf SNP realignment
5.0 years ago by Siavash Salek Ardestani ▴ 20
9
votes
16
replies
1.3k
views
feature extraction from SNPs in R
R gene sequence SNP
4.4 years ago by bioinfo456 ▴ 150
2
votes
16
replies
2.4k
views
Enhancing draft genome using 10X data
10X draft_genome Assembly
4.6 years ago by Mostafa ▴ 20
0
votes
16
replies
3.6k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 8 months ago by 38k • written 7.9 years ago by ▴ 550
5
votes
16
replies
3.4k
views
plotting problem with loop in R
R plot
3.8 years ago by smyiz ▴ 30
14
votes
16
replies
1.3k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 2.4 years ago by 14k • written 2.4 years ago by ▴ 80
13
votes
16
replies
5.4k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
4.2 years ago by DNAngel ▴ 240
7
votes
16
replies
17k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
6.6 years ago by aggregatibacter ▴ 170
5
votes
16
replies
2.6k
views
Hisat2 aligner problem
RNA-Seq ChIP-Seq alignment Assembly software error
3.8 years ago by ta_awwad ▴ 320
2
votes
16
replies
3.9k
views
Working with human database in Kraken
RNA-Seq next-gen genome
6.8 years ago by Ron ★ 1.1k
2
votes
16
replies
9.4k
views
Tophat with Bowtie2 long index
tophat bowtie
updated 14 months ago by 38k • written 8.7 years ago by ▴ 130
5
votes
16
replies
4.8k
views
Remove duplicate lines based on specific columns
r python intersect reads
updated 4.5 years ago by 38k • written 4.5 years ago by ▴ 60
4
votes
16
replies
1.1k
views
How to extract intron counts from total RNA Sequencing?
featurecounts RNAseq htseq STAR
4 months ago by barrypraveen ▴ 100
7
votes
16
replies
2.7k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing genome-sequence fastqc genome sequence
3.0 years ago by Negin ▴ 20
13
votes
16
replies
4.9k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
6.2 years ago by Paul ★ 1.5k
0
votes
16
replies
4.5k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools sort
9.8 years ago by chentong.biology ▴ 50
0
votes
16
replies
3.0k
views
Gff to genbank - feature is missing
gff3 genbank DNA augustus bioinformatics
updated 4.6 years ago by 20 • written 4.8 years ago by • 0
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 1 day ago by 38k • written 4.6 years ago by ▴ 670
0
votes
16
replies
2.7k
views
Problems with installation of Prodege decontamination software
genome next-gen sequencing sequence blast
updated 6.1 years ago by 20 • written 6.2 years ago by • 0
1,000 results • Page 3 of 20
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Answer: PCA in gene expression
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Comment: bioinformatics problems solved by graphs data structure by lieven.sterck 14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts by lieven.sterck 14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that…
Answer: How to analize multiple letters codes in COG IDs? by Mensur Dlakic ★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene? by sunyeping ▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file? by Pierre Lindenbaum 153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs? by Darked89 4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
Comment: ExomeDepth installation error by Medha • 0
Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam fil…
Comment: ExomeDepth installation error by jared.andrews07 ★ 14k
No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.
Comment: ExomeDepth installation error by Medha • 0
Hi @jaredandrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rs…
Comment: Embedded stop codon in translated nucleotide sequences in DAMBE by Mensur Dlakic ★ 23k
It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading fr…
Comment: Error with a function in ATAC-seq analysis by Chris ▴ 70
So you skip the GRanges()? Yes, no error anymore but I am not sure if that causes changing in downstream analysis.
Answer: ClusterProfiler enrichKEGG – remove organism name in plots? by jv ★ 1.0k
`stringr::str_remove` can remove " - Mus musculus (house mouse)" from the pathway names which are stored under `KEGGPATHID2NAME$to` in your…
Comment: Error with a function in ATAC-seq analysis by jv ★ 1.0k
run `union` on the data frames
Comment: PCA in gene expression by ali • 0
Thanks for your attention. yes I know that we should not omit the samples, I just worry about noises on my differential expression and some…
Comment: Error with a function in ATAC-seq analysis by Chris ▴ 70
Yes, it is not a vector. Formal class 'GRanges' Because GRanges() function made it become a Granges class which is a data frame before tha…
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