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1,000 results • Page 4 of 20
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4
votes
16
replies
4.2k
views
Working with human database in Kraken
RNA-Seq next-gen genome
7.3 years ago by Ron ★ 1.1k
9
votes
16
replies
1.2k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.1 years ago by 14k • written 3.1 years ago by ▴ 150
5
votes
16
replies
3.8k
views
plotting problem with loop in R
R plot
4.3 years ago by smyiz ▴ 30
4
votes
16
replies
5.9k
views
How to count occurrence of numbers in text files using phython
python excel counting writelines
6.7 years ago by Kachibunny • 0
8
votes
16
replies
1.2k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene next-gen
3.7 years ago by Chaimaa ▴ 260
4
votes
16
replies
1.8k
views
How to extract intron counts from total RNA Sequencing?
featurecounts RNAseq htseq STAR
10 months ago by barrypraveen ▴ 110
13
votes
16
replies
5.4k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
6.7 years ago by Paul ★ 1.5k
5
votes
16
replies
3.1k
views
Hisat2 aligner problem
RNA-Seq ChIP-Seq alignment Assembly software error
4.3 years ago by ta_awwad ▴ 340
1
vote
16
replies
2.3k
views
Merging fastq files from two experiments
FASTQ NGS
updated 4.6 years ago by 20 • written 4.7 years ago by ★ 4.2k
0
votes
16
replies
2.9k
views
Problems with installation of Prodege decontamination software
genome next-gen sequencing sequence blast
updated 6.6 years ago by 20 • written 6.7 years ago by • 0
2
votes
16
replies
9.7k
views
Tophat with Bowtie2 long index
tophat bowtie
updated 20 months ago by 40k • written 9.2 years ago by ▴ 140
13
votes
16
replies
6.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
4.7 years ago by DNAngel ▴ 240
2
votes
16
replies
1.6k
views
I want to know is it a true method ?
vcf SNP realignment
5.5 years ago by Siavash Salek Ardestani ▴ 20
7
votes
16
replies
2.4k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 6 months ago by 40k • written 6.0 years ago by ★ 3.6k
0
votes
16
replies
2.1k
views
How to convert ncbi gff file to ensembl gff format
bcftools gff
updated 6 months ago by 40k • written 13 months ago by ▴ 10
7
votes
16
replies
19k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
7.1 years ago by aggregatibacter ▴ 180
4
votes
16
replies
8.3k
views
STAR - genome indexes generation, genome file not created
RNA-Seq star
updated 4.1 years ago by 20 • written 6.9 years ago by ▴ 70
1
vote
16
replies
1.7k
views
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
RNA-Seq hisat2 samtools mapping
updated 5.3 years ago by 20 • written 5.4 years ago by ▴ 730
4
votes
15
replies
3.7k
views
Paired-read alignment length from BAM/SAM file
bam sam paired-read alignment
6.3 years ago by Soumitra Pal ▴ 10
5
votes
15
replies
1.4k
views
NGS Sequencing depths
next-gen sequencing gene
6.6 years ago by sliproach ▴ 10
10
votes
15
replies
5.8k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast MEGAN6 Taxonomy DIAMOND
6.8 years ago by Farbod ★ 3.4k
1
vote
15
replies
2.8k
views
How to perform multiple alignment using MAFFT?
genome alignment gene sequence
2.4 years ago by anikcropscience ▴ 180
4
votes
15
replies
2.8k
views
Adding Multiple readgroups to BAM file
GATK ReadGroups
7.4 years ago by vakul.mohanty ▴ 270
1
vote
15
replies
4.7k
views
How to Extract Specific Region on Bam file
Nanopore HG38 Rna-Seq Genome
updated 2.3 years ago by 86k • written 2.3 years ago by ▴ 40
1
vote
15
replies
4.1k
views
Ultrafast alignment of short sequences to a genome (with up to 5 mismatches!)
genome alignment
updated 21 months ago by 40k • written 9.0 years ago by ▴ 360
5
votes
15
replies
1.6k
views
Testing uniform distribution of SNPs across chromosome
uniform vcf SNP
4.4 years ago by misterie ▴ 110
1
vote
15
replies
1.1k
views
Single Cell RNA Seq
scTransform Harmony scRNAseq Seurat
5 weeks ago by scRNA2023 • 0
0
votes
15
replies
2.6k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 22 months ago by ▴ 20 • written 2.2 years ago by ▴ 20
6
votes
15
replies
1.4k
views
Reads partly within an exon
RNA-Seq
6.2 years ago by benjyrolls ▴ 70
5
votes
15
replies
1.2k
views
Get list of gene signatures published
bailey genes subtype pancreas
2.7 years ago by sabin ▴ 50
2
votes
15
replies
3.9k
views
How to interpret reads mapped to genome from samtools flagstat vs TopHat align_summary.txt ?
RNA-Seq
7.4 years ago by Vasu ▴ 730
0
votes
15
replies
1.7k
views
Chromosome accession numbers correspond to which chromosome?
bam chromosome bed
10 months ago by amy__ ▴ 150
5
votes
15
replies
4.9k
views
Annotation with snpEFF
annotation vcf snpeff extractFields
updated 5.2 years ago by 20 • written 5.3 years ago by ▴ 960
6
votes
15
replies
2.1k
views
processing in strelka2 with multiples bam file in directory
strelka2
updated 20 months ago by ▴ 70 • written 3.8 years ago by ▴ 230
1
vote
15
replies
1.2k
views
How to reduce my dataset in order to plot it?
correlation igraph
updated 4.1 years ago by 20 • written 4.3 years ago by ▴ 280
1
vote
15
replies
1.5k
views
Samtools merge Illumina and PB bam file empty
Illumina samtools Bam PacBio
updated 6 months ago by 40k • written 3.1 years ago by • 0
0
votes
15
replies
2.3k
views
Strategy for generating a consensus sequence for 100 complete bacterial genomes?
consensus seq mauve
5.3 years ago by Alec Watanabe ▴ 60
0
votes
15
replies
2.8k
views
how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
RNA-Seq
6.0 years ago by genya35 ▴ 40
0
votes
15
replies
1.7k
views
compare two NCBI ftp tables
table NCBI
updated 2.3 years ago by 40k • written 2.3 years ago by ▴ 20
0
votes
15
replies
2.1k
views
pathway analysis tools for xenopus
pathways omics xenopus
updated 7.2 years ago by 7.5k • written 7.2 years ago by ▴ 90
2
votes
15
replies
932
views
Manipulate refseq database
ncbi database nt refseq
updated 3.6 years ago by 20 • written 3.7 years ago by ▴ 80
3
votes
15
replies
5.2k
views
Pairwise sequence alignment with Biojava?
sequence-alignment biojava java
updated 20 months ago by 40k • written 8.9 years ago by ▴ 360
7
votes
15
replies
5.9k
views
6 follow
blastn error - NCBI C++ Exception
assembly blast alignment
updated 18 months ago by 14k • written 2.5 years ago by ▴ 970
6
votes
15
replies
2.7k
views
Why GSVA returns a matrix with fewer gene-sets?
microarray GSVA
updated 21 months ago by ▴ 70 • written 5.5 years ago by ▴ 280
5
votes
15
replies
7.8k
views
Strand specific protocol for bowtie2 alignment
bowtie2 rnaseq alignment RNA-Seq
updated 22 months ago by 40k • written 7.9 years ago by ▴ 90
6
votes
15
replies
1.3k
views
The Best Cloud Solution For Genomics
cloud data-sharing genomics workflow
updated 14 months ago by 40k • written 15 months ago by ▴ 50
11
votes
15
replies
2.5k
views
How do I get the read counts for a specific exon
bam exon
updated 5.5 years ago by 40k • written 5.5 years ago by ▴ 30
1
vote
15
replies
3.4k
views
Fastx quality filter
next-gen RNA-Seq software error sequencing
updated 6.8 years ago by 40k • written 6.8 years ago by ▴ 10
1
vote
15
replies
3.5k
views
Can I use PICARD (SortSam) instead of SAMTOOLS (sort) for sorting bam files in RNAseq pipeline where HISAT2 is used for alignment.
RNA-Seq software error sequencing next-gen
5.4 years ago by shuksi1984 ▴ 60
10
votes
15
replies
5.6k
views
convert fasta/gb to vcf
fasta vcf genbank gff
updated 6 months ago by 40k • written 5.0 years ago by ▴ 690
1,000 results • Page 4 of 20
Recent Votes
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
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
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Recent Replies
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)
Comment: Merging the filename with tsv files for master file by barslmn ★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ? by barslmn ★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase by Barry Digby ★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups by ATpoint 76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups by edus_bioinfo ▴ 40
To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise by ATpoint 76k
You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups by Basti ★ 1.7k
Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file by Patrick • 0
Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
Answer: Average Coverage after Assembly (Spades) by taniapsduarte • 0
Hi, I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!
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