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1,000 results • Page 3 of 20
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3
votes
17
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1.1k
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copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV DownSample fastq copy number not accurate
3.3 years ago by lffu_0032 ▴ 90
3
votes
17
replies
5.6k
views
Removing fastq duplicates
sequence next-gen ChIP-Seq
2.5 years ago by C4 ▴ 10
6
votes
17
replies
1.9k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen assembly genome alignment
5.0 years ago by williamsbrian5064 ▴ 470
0
votes
17
replies
2.5k
views
I am not able to let R read my file
R fasta
updated 2.2 years ago by 3.2k • written 2.2 years ago by • 0
7
votes
17
replies
6.0k
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
4.9 years ago by WUSCHEL ▴ 720
7
votes
17
replies
3.7k
views
Strange MA-plot using DESeq2
rna-seq R deseq2
updated 6.4 years ago by 20 • written 6.5 years ago by ▴ 80
0
votes
17
replies
2.3k
views
Fail running blastdb and blastn on my own computer
blast
5.6 years ago by annette440 • 0
5
votes
17
replies
3.7k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics encode
9.2 years ago by 14134125465346445 ★ 3.6k
0
votes
17
replies
4.2k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 8 months ago by 39k • written 7.7 years ago by ▴ 30
1
vote
17
replies
5.2k
views
BBMap: Mapping Fails
BBTools BBMap Mapping
updated 7.2 years ago by 129k • written 7.2 years ago by ▴ 50
1
vote
17
replies
3.4k
views
Error executing bedops convert2bed
bedops bed vcf convert2bed
6.4 years ago by lakhujanivijay 5.7k
4
votes
17
replies
2.3k
views
Cufflinks analysis and gffread
RNA-Seq Assembly
updated 5.6 years ago by 85k • written 5.6 years ago by ▴ 100
27
votes
17
replies
17k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
18 months ago by Leite ★ 1.2k
12
votes
17
replies
4.0k
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
5.6 years ago by anonymous1192976466 ▴ 50
16
votes
17
replies
2.7k
views
6 follow
RNA seq pipeline
RNA-Seq
5.6 years ago by dimitrischat ▴ 180
9
votes
17
replies
1.8k
views
Creating intergenic bam file
R genome intergenic alignment
6.8 years ago by erincyurtman • 0
0
votes
17
replies
3.0k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq wgcna software error R next-gen
updated 17 months ago by • 0 • written 4.7 years ago by ▴ 20
8
votes
17
replies
3.4k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
5.3 years ago by Sharon ▴ 590
7
votes
17
replies
3.2k
views
How to find the differences in aligned bam files
RNA-Seq
6.3 years ago by 1769mkc ★ 1.1k
2
votes
17
replies
2.0k
views
Snakemake Megahit error
megahit Snakemake
18 months ago by blackadder ▴ 20
2
votes
17
replies
4.5k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 5.2 years ago by 34k • written 5.2 years ago by ▴ 30
3
votes
17
replies
2.4k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
2.2 years ago by boczniak767 ▴ 830
4
votes
17
replies
2.2k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray gene-expression CV error
3.9 years ago by Jurat Shahidin ▴ 100
1
vote
17
replies
2.1k
views
Normalizing BLAST results
blast
updated 5.7 years ago by 20 • written 5.8 years ago by • 0
2
votes
17
replies
3.9k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam bam alignment samtools
updated 9.4 years ago by 103k • written 9.4 years ago by ★ 1.5k
2
votes
17
replies
6.7k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping genome fastq STAR
updated 15 months ago by • 0 • written 2.4 years ago by • 0
7
votes
16
replies
3.0k
views
How do I get a GFF file
snp
3.9 years ago by apl00028 ▴ 70
0
votes
16
replies
4.0k
views
Issue using MaSuRCA-3.2.6
Assembly assembler
updated 4.8 years ago by 20 • written 5.0 years ago by ▴ 100
3
votes
16
replies
975
views
How to bring all reads to the same length? Any tool?
Read length Bed Tool
3.4 years ago by Ankit ▴ 390
3
votes
16
replies
3.2k
views
GC content of 10x Genomics
fastqc 10x GC content
updated 2.8 years ago by ▴ 170 • written 4.1 years ago by ★ 1.8k
9
votes
16
replies
973
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 2.8 years ago by 14k • written 2.8 years ago by ▴ 150
9
votes
16
replies
1.4k
views
feature extraction from SNPs in R
R gene sequence SNP
4.6 years ago by bioinfo456 ▴ 150
5
votes
16
replies
5.1k
views
Remove duplicate lines based on specific columns
r python intersect reads
updated 4.7 years ago by 39k • written 4.7 years ago by ▴ 60
7
votes
16
replies
2.1k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 9 weeks ago by 39k • written 5.6 years ago by ★ 3.6k
0
votes
16
replies
1.7k
views
How to convert ncbi gff file to ensembl gff format
bcftools gff
updated 10 weeks ago by 39k • written 9 months ago by ▴ 10
1
vote
16
replies
5.3k
views
After sorting bam file not able to index ?
alignment next-gen
updated 4.3 years ago by 20 • written 4.4 years ago by ▴ 970
5
votes
16
replies
2.8k
views
Hisat2 aligner problem
RNA-Seq ChIP-Seq alignment Assembly software error
4.0 years ago by ta_awwad ▴ 320
7
votes
16
replies
2.9k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing genome-sequence fastqc genome sequence
3.2 years ago by Negin ▴ 20
5
votes
16
replies
2.1k
views
a lot of OTUs wth no reference
16S
5.6 years ago by agata88 ▴ 850
0
votes
16
replies
3.7k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 11 months ago by 39k • written 8.1 years ago by ▴ 550
9
votes
16
replies
3.0k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 10 weeks ago by 39k • written 4.8 years ago by ▴ 680
3
votes
16
replies
2.8k
views
FastTree trifurcating Root node
alignment FastTree Phylogenetic Tree
4.4 years ago by Moses ▴ 140
3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel R statistics
updated 3 days ago by 39k • written 4.2 years ago by ▴ 60
0
votes
16
replies
4.6k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools sort
10.0 years ago by chentong.biology ▴ 50
8
votes
16
replies
1.1k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene next-gen
3.4 years ago by Chaimaa ▴ 260
4
votes
16
replies
8.1k
views
STAR - genome indexes generation, genome file not created
RNA-Seq star
updated 3.7 years ago by 20 • written 6.5 years ago by ▴ 70
16
votes
16
replies
2.5k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
5.2 years ago by bioinfo456 ▴ 150
7
votes
16
replies
18k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
6.8 years ago by aggregatibacter ▴ 180
3
votes
16
replies
4.0k
views
Working with human database in Kraken
RNA-Seq next-gen genome
7.0 years ago by Ron ★ 1.1k
5
votes
16
replies
3.5k
views
plotting problem with loop in R
R plot
4.0 years ago by smyiz ▴ 30
1,000 results • Page 3 of 20
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Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data by Hamid Ghaedi 2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP by Vincent Laufer ★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs by rycro_c • 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage by Dave Carlson ★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order? by Pierre Lindenbaum 154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage by GenoMax 129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files by Joe 21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig by GenoMax 129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order? by GenoMax 129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column by atemedorri137798 • 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order? by Ram 39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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