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1,000 results • Page 3 of 20
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2
votes
18
replies
1.7k
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error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
7 weeks ago by b.contreras.moreira ▴ 200
5
votes
18
replies
6.8k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R EnhancedVolcano
4.5 years ago by michelle.piquet ▴ 60
3
votes
18
replies
3.3k
views
Help creating Deseq2 count matrix from separate files
or Sample matrix
updated 2.8 years ago by 43k • written 2.9 years ago by ▴ 50
16
votes
18
replies
5.6k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.7 years ago by ★ 27k • written 4.7 years ago by • 0
2
votes
18
replies
2.8k
views
Bwa on multiple processor
np mpirun bwa alignment
2.4 years ago by shivangi.agarwal800 ▴ 120
14
votes
18
replies
2.4k
views
Clustering in single cell
seurat single-cell
updated 7 months ago by ▴ 210 • written 7 months ago by ▴ 280
4
votes
18
replies
4.2k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq virus reads fusion
updated 21 months ago by 43k • written 8.5 years ago by ▴ 60
14
votes
18
replies
5.0k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 7.4 years ago by 20 • written 7.6 years ago by ▴ 50
0
votes
18
replies
1.9k
views
bcl2fastq conversion with specifying exact match of indices
genome RNA-Seq sequencing
updated 9 months ago by 142k • written 9 months ago by ▴ 280
20
votes
17
replies
6.1k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
6.8 years ago by Anand Rao ▴ 630
7
votes
17
replies
4.3k
views
Strange MA-plot using DESeq2
rna-seq R deseq2
updated 7.3 years ago by 20 • written 7.5 years ago by ▴ 80
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.6 years ago by dimitrischat ▴ 210
0
votes
17
replies
3.7k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq wgcna software error R next-gen
updated 2.4 years ago by • 0 • written 5.6 years ago by ▴ 20
5
votes
17
replies
4.3k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics encode
10.2 years ago by 14134125465346445 ★ 3.6k
3
votes
17
replies
2.9k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
3.1 years ago by boczniak767 ▴ 850
6
votes
17
replies
2.4k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen assembly genome alignment
5.9 years ago by williamsbrian5064 ▴ 520
0
votes
17
replies
1.5k
views
Transcripts with no read support
RNA-Seq alignment assembly salmon
3.7 years ago by Dunois ★ 2.5k
12
votes
17
replies
4.9k
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
6.6 years ago by anonymous1192976466 ▴ 50
1
vote
17
replies
2.4k
views
Normalizing BLAST results
blast
updated 6.6 years ago by 20 • written 6.8 years ago by • 0
2
votes
17
replies
5.1k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 30
20
votes
17
replies
3.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by ★ 1.2k • written 3.3 years ago by ▴ 110
0
votes
17
replies
5.0k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 20 months ago by 43k • written 8.7 years ago by ▴ 30
2
votes
17
replies
2.9k
views
Snakemake Megahit error
megahit Snakemake
2.5 years ago by blackadder ▴ 30
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
6.3 years ago by Sharon ▴ 610
2
votes
17
replies
4.4k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam bam alignment samtools
updated 10.4 years ago by 104k • written 10.4 years ago by ★ 1.5k
4
votes
17
replies
2.9k
views
Cufflinks analysis and gffread
RNA-Seq Assembly
updated 6.5 years ago by 88k • written 6.6 years ago by ▴ 100
9
votes
17
replies
2.2k
views
Creating intergenic bam file
R genome intergenic alignment
7.8 years ago by erincyurtman • 0
7
votes
17
replies
6.6k
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
5.9 years ago by WUSCHEL ▴ 760
2
votes
17
replies
9.9k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping genome fastq STAR
updated 2.2 years ago by • 0 • written 3.4 years ago by • 0
0
votes
17
replies
3.1k
views
I am not able to let R read my file
R fasta
updated 3.2 years ago by 3.2k • written 3.2 years ago by • 0
0
votes
17
replies
2.8k
views
Fail running blastdb and blastn on my own computer
blast
6.5 years ago by annette440 • 0
1
vote
17
replies
4.3k
views
Error executing bedops convert2bed
bedops bed vcf convert2bed
7.3 years ago by lakhujanivijay 5.8k
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
2.5 years ago by Leite ★ 1.3k
3
votes
17
replies
1.6k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV DownSample fastq copy number not accurate
4.3 years ago by lffu_0032 ▴ 90
5
votes
17
replies
8.7k
views
Removing fastq duplicates
sequence next-gen ChIP-Seq
3.5 years ago by C4 ▴ 30
4
votes
17
replies
2.8k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray gene-expression CV error
4.9 years ago by Jurat Shahidin ▴ 100
7
votes
17
replies
3.9k
views
How to find the differences in aligned bam files
RNA-Seq
7.2 years ago by 1769mkc ★ 1.2k
0
votes
17
replies
1.2k
views
Issues while running htseq-count
Candida-glabrata RNA-seq htseq-count
4 months ago by Foad ▴ 10
1
vote
17
replies
5.8k
views
BBMap: Mapping Fails
BBTools BBMap Mapping
updated 8.2 years ago by 142k • written 8.2 years ago by ▴ 60
7
votes
16
replies
3.7k
views
How do I get a GFF file
snp
4.9 years ago by apl00028 ▴ 90
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly assembler
updated 5.7 years ago by 20 • written 5.9 years ago by ▴ 130
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length Bed
updated 11 months ago by 43k • written 4.3 years ago by ▴ 500
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment FastTree Phylogenetic Tree
5.4 years ago by Moses ▴ 150
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.8 years ago by 15k • written 3.8 years ago by ▴ 160
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X draft_genome Assembly
5.8 years ago by Mostafa ▴ 20
8
votes
16
replies
1.5k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene next-gen
4.4 years ago by Chaimaa ▴ 260
9
votes
16
replies
2.0k
views
feature extraction from SNPs in R
R gene sequence SNP
5.5 years ago by bioinfo456 ▴ 150
13
votes
16
replies
7.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
5.4 years ago by DNAngel ▴ 250
1
vote
16
replies
7.1k
views
After sorting bam file not able to index ?
alignment next-gen
updated 5.3 years ago by 20 • written 5.4 years ago by ▴ 980
16
votes
16
replies
3.2k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
6.2 years ago by bioinfo456 ▴ 150
1,000 results • Page 3 of 20
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Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
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A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
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Comment: What is the amount of sequencing data produced annually? by Mohamed • 0
Here's a more neat version of the plot generated while writing my dissertation: ![enter image description here][1] [1]: https://raw.gi…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
what a pity...
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Yes, I can. But there are only two factors that affect my data PCA distribution: groups and donor. And the rest is regarded as residual. …
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by colindaven 6.4k
Please delete this as it has nothing to do with the topic of this forum, bioinformatics. Thanks
Comment: Add stats to the plot by marco.barr ▴ 130
if don't work try binding the stats without group. stat_data4 <- data4.ts %>% ungroup() %>% t.test(data = ., value ~ Cond…
Comment: Nextflow docker: Error response from daemon by Pierre Lindenbaum 161k
you should ask : https://github.com/nf-core/sarek/issues/
Comment: Where to find old version of GATK best practice by Pierre Lindenbaum 161k
https://github.com/gatk-workflows ?
Comment: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
Hi, if you can please post a separate question with inputs and expected output, reply here with a link to it, and I'll take a look.
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Hi again Alex, sorry to ask another question about this, but how can I tweak this code to keep **all** of the SNPs that pass the threshold …
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Hello I have a quick question, I did as you said , and further added the traits, found the correlation among the modules and the traits us…
Comment: Elbow plot question (scRNA seq data analysis - scanpy tutorial) by ojaswinipandey • 0
Thank you so much Dave.
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial) by Dave Carlson ★ 1.7k
The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between…
Comment: Error in using BioSampleParser tool: subscript out of bounds by marco.barr ▴ 130
Hi Mohamed, I also thought the same thing but we run the risk of inserting other errors perhaps by modifying the function. I tried but I ha…
Comment: Trimming tool by Ram 43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by Ram 43k
This post does not fit the theme of this forum.
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