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1,000 results • Page 3 of 20
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7
votes
18
replies
4.2k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie alignment genome
6.9 years ago by valerie ▴ 100
0
votes
18
replies
1.1k
views
bcl2fastq conversion with specifying exact match of indices
genome RNA-Seq sequencing
updated 4 weeks ago by 134k • written 4 weeks ago by ▴ 270
20
votes
17
replies
5.5k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
6.1 years ago by Anand Rao ▴ 570
0
votes
17
replies
3.3k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq wgcna software error R next-gen
updated 21 months ago by • 0 • written 5.0 years ago by ▴ 20
4
votes
17
replies
2.4k
views
Cufflinks analysis and gffread
RNA-Seq Assembly
updated 5.9 years ago by 86k • written 5.9 years ago by ▴ 100
1
vote
17
replies
2.2k
views
Normalizing BLAST results
blast
updated 6.0 years ago by 20 • written 6.1 years ago by • 0
3
votes
17
replies
1.2k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV DownSample fastq copy number not accurate
3.6 years ago by lffu_0032 ▴ 90
0
votes
17
replies
2.7k
views
I am not able to let R read my file
R fasta
updated 2.5 years ago by 3.2k • written 2.5 years ago by • 0
3
votes
17
replies
6.7k
views
Removing fastq duplicates
sequence next-gen ChIP-Seq
2.8 years ago by C4 ▴ 10
0
votes
17
replies
4.4k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 12 months ago by 40k • written 8.0 years ago by ▴ 30
5
votes
17
replies
3.9k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics encode
9.6 years ago by 14134125465346445 ★ 3.6k
6
votes
17
replies
2.1k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen assembly genome alignment
5.3 years ago by williamsbrian5064 ▴ 480
16
votes
17
replies
2.9k
views
6 follow
RNA seq pipeline
RNA-Seq
5.9 years ago by dimitrischat ▴ 200
1
vote
17
replies
5.4k
views
BBMap: Mapping Fails
BBTools BBMap Mapping
updated 7.5 years ago by 134k • written 7.5 years ago by ▴ 50
27
votes
17
replies
19k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
21 months ago by Leite ★ 1.2k
2
votes
17
replies
2.3k
views
Snakemake Megahit error
megahit Snakemake
22 months ago by blackadder ▴ 30
2
votes
17
replies
4.0k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam bam alignment samtools
updated 9.7 years ago by 103k • written 9.7 years ago by ★ 1.5k
1
vote
17
replies
3.6k
views
Error executing bedops convert2bed
bedops bed vcf convert2bed
6.7 years ago by lakhujanivijay 5.8k
7
votes
17
replies
3.9k
views
Strange MA-plot using DESeq2
rna-seq R deseq2
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 80
0
votes
17
replies
2.4k
views
Fail running blastdb and blastn on my own computer
blast
5.9 years ago by annette440 • 0
3
votes
17
replies
2.6k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
2.5 years ago by boczniak767 ▴ 840
12
votes
17
replies
4.2k
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
6.0 years ago by anonymous1192976466 ▴ 50
0
votes
17
replies
1.2k
views
Transcripts with no read support
RNA-Seq alignment assembly salmon
3.0 years ago by Dunois ★ 2.4k
9
votes
17
replies
1.9k
views
Creating intergenic bam file
R genome intergenic alignment
7.1 years ago by erincyurtman • 0
4
votes
17
replies
2.4k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray gene-expression CV error
4.2 years ago by Jurat Shahidin ▴ 100
8
votes
17
replies
3.6k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
5.6 years ago by Sharon ▴ 590
7
votes
17
replies
3.5k
views
How to find the differences in aligned bam files
RNA-Seq
6.6 years ago by 1769mkc ★ 1.1k
7
votes
17
replies
6.2k
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
5.2 years ago by WUSCHEL ▴ 720
2
votes
17
replies
7.9k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping genome fastq STAR
updated 18 months ago by • 0 • written 2.7 years ago by • 0
2
votes
17
replies
4.7k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 5.5 years ago by 34k • written 5.5 years ago by ▴ 30
20
votes
17
replies
2.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 11 weeks ago by ★ 1.1k • written 2.6 years ago by ▴ 110
7
votes
16
replies
3.2k
views
How do I get a GFF file
snp
4.3 years ago by apl00028 ▴ 80
0
votes
16
replies
4.2k
views
Issue using MaSuRCA-3.2.6
Assembly assembler
updated 5.1 years ago by 20 • written 5.3 years ago by ▴ 120
3
votes
16
replies
1.2k
views
How to bring all reads to the same length? Any tool?
Read-length Bed
updated 3 months ago by 40k • written 3.7 years ago by ▴ 390
3
votes
16
replies
11k
views
combining z-scores into a single z-score value
excel R statistics
updated 3 months ago by 40k • written 4.5 years ago by ▴ 60
3
votes
16
replies
3.5k
views
GC content of 10x Genomics
fastqc 10x GC content
updated 3.1 years ago by ▴ 170 • written 4.5 years ago by ★ 1.8k
1
vote
16
replies
6.1k
views
After sorting bam file not able to index ?
alignment next-gen
updated 4.6 years ago by 20 • written 4.7 years ago by ▴ 970
9
votes
16
replies
1.5k
views
feature extraction from SNPs in R
R gene sequence SNP
4.9 years ago by bioinfo456 ▴ 150
7
votes
16
replies
3.3k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing genome-sequence fastqc genome sequence
3.5 years ago by Researcher ▴ 20
2
votes
16
replies
2.7k
views
Enhancing draft genome using 10X data
10X draft_genome Assembly
5.1 years ago by Mostafa ▴ 20
0
votes
16
replies
3.4k
views
Gff to genbank - feature is missing
DNA augustus gff3 genbank
updated 4 months ago by 40k • written 5.3 years ago by • 0
3
votes
16
replies
1.2k
views
Problem, getting information only from the last row and not from all the rows
perl
5.4 years ago by ArusjakGevorgyan ▴ 30
0
votes
16
replies
4.8k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools sort
10.4 years ago by chentong.biology ▴ 50
16
votes
16
replies
2.7k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
5.5 years ago by bioinfo456 ▴ 150
9
votes
16
replies
3.3k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 6 months ago by 40k • written 5.1 years ago by ▴ 690
5
votes
16
replies
2.3k
views
a lot of OTUs wth no reference
16S
5.9 years ago by agata88 ▴ 860
0
votes
16
replies
3.9k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 14 months ago by 40k • written 8.4 years ago by ▴ 550
14
votes
16
replies
1.6k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 2.9 years ago by 14k • written 2.9 years ago by ▴ 80
3
votes
16
replies
3.0k
views
FastTree trifurcating Root node
alignment FastTree Phylogenetic Tree
4.7 years ago by Moses ▴ 140
5
votes
16
replies
5.5k
views
Remove duplicate lines based on specific columns
r python intersect reads
updated 5.0 years ago by 40k • written 5.0 years ago by ▴ 60
1,000 results • Page 3 of 20
Recent Votes
Comment: Quantification after transcriptome assembly with Trinity
Snakemake: output folder a as dependency to a different rule
A: Snakemake: output folder a as dependency to a different rule
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
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Comment: Calculation of TMB on gene level by smrutimayipanda ▴ 20
can you please tell me why it is technically incorrect?
Answer: Gene enrichment analysis of prokaryotes gene by dthorbur ▴ 550
[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses. [H…
Comment: Read block operation failed with BAM file by John Marshall 3.0k
Indeed, though it is a seek issue when accessing files **over HTTP and other network protocols**. So, unless there's something you didn't m…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by RM123 ▴ 10
Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups by ATpoint 76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups by edus_bioinfo ▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype by dthorbur ▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by RM123 ▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R by Nicolas Rosewick 10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting by fracarb8 ★ 1.2k
You did not add the screenshot.
Answer: BED files by Alex Reynolds 35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by dariober 14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files by barslmn ★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors by Alex Reynolds 35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file by Alex Reynolds 35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
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