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565 results • Page 2 of 12
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7
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9 follow
Forum: Dentist interested in bioinformatics
career
updated 1 day ago by ★ 2.6k • written 7.7 years ago by ▴ 10
28
votes
8
replies
16k
views
Use samtools index on multiple bam files at the same time from the command line?
RNA-Seq next-gen sequence
updated 13 days ago by 163k • written 8.7 years ago by ▴ 490
3
votes
8
replies
4.0k
views
WGCNA adjust p value
statistics WGCNA
updated 11 days ago by • 0 • written 3.1 years ago by ▴ 10
6
votes
8
replies
559
views
How to perform BLASTn on a large 348kb phage genome?
BLASTn
updated 13 days ago by 145k • written 13 days ago by • 0
5
votes
8
replies
2.1k
views
6 follow
Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
CRAM Nebula samtools
updated 1 day ago by ▴ 110 • written 24 months ago by ▴ 70
5
votes
7
replies
3.5k
views
Status of maker annotation
genome annotation maker
updated 4 days ago by 8.7k • written 8.3 years ago by ★ 2.7k
3
votes
7
replies
441
views
How to create a tax_id_map file for getting scientific names in BLASTN output
BLAST NCBI
18 days ago by Maria • 0
9
votes
7
replies
4.3k
views
How to select differential expressed genes using DeSeq2?
RNA-Seq R gene
updated 12 days ago by ▴ 10 • written 3.9 years ago by ▴ 60
2
votes
7
replies
497
views
How to check coverage in bam file?
bam
updated 10 days ago by ★ 3.9k • written 10 days ago by ▴ 50
2
votes
7
replies
849
views
BUSCO v3 eukaryotic database
genome assembly BUSCO
updated 25 days ago by 145k • written 8 months ago by • 0
2
votes
7
replies
2.3k
views
Separate single cell BAM file by the cell barcode
BAM scRNAseq single-cell
updated 29 days ago by • 0 • written 13 months ago by ▴ 30
4
votes
7
replies
2.1k
views
bbsplit running slow or out of memory?
next-gen-sequencing RNA-Seq WES ATAC-seq
updated 4 days ago by ▴ 90 • written 3.6 years ago by ▴ 60
7
votes
7
replies
2.2k
views
How does the DNA-seq machine know which strand that is forward/reverse?
dna-seq
updated 1 day ago by ▴ 640 • written 2.8 years ago by ▴ 40
1
vote
7
replies
531
views
Core_nt database not available to download?
blast ncbi
updated 9 days ago by 145k • written 10 days ago by ▴ 250
2
votes
7
replies
676
views
Generate Max Number of DNA Sequences separated by a given Hamming distance
hamming-distance Barcode variants DNA
12 days ago by rtrende ▴ 80
1
vote
7
replies
1.4k
views
(hmmsearch) find targets with multiple query profiles with hmmsearch
multiple hmmer queries hmmsearch profiles
updated 1 day ago by ★ 28k • written 2.8 years ago by ▴ 10
0
votes
7
replies
265
views
KeepBothReads in Trimmomatic
Trimmomatic PE-reads
updated 1 day ago by 145k • written 1 day ago by ▴ 90
6
votes
7
replies
578
views
Hard to automatically download NCBI protein IDs
NCBI batch-download
updated 16 days ago by 44k • written 19 days ago by ▴ 180
9
votes
7
replies
6.7k
views
How to generate sequence length distribution from Fasta file
RNA-Seq sRNA-seq fatsa
updated 19 hours ago by ▴ 140 • written 4.6 years ago by ▴ 120
5
votes
7
replies
9.1k
views
6 follow
pathway for single cell RNA-seq
pathway
updated 27 days ago by • 0 • written 6.6 years ago by ★ 1.2k
1
vote
7
replies
3.0k
views
average depth of each region in a BED file calculated from a BAM file
BED BAM coverage NGS
updated 27 days ago by • 0 • written 4.1 years ago by ▴ 170
1
vote
6
replies
1.5k
views
Cacoa with Seurat analysis
cacoa differential-abundance Seurat
updated 5 days ago by 145k • written 11 months ago by • 0
0
votes
6
replies
399
views
Batch correction for RNA-seq using ComBat-seq for same group and batch
SVA ComBat_seq ComBat DESeq2 RNA-seq
23 days ago by botloggy ▴ 10
3
votes
6
replies
1.3k
views
GGtree flips my tree
ggtree phylogenetics R
updated 4 days ago by 44k • written 13 months ago by ▴ 40
0
votes
6
replies
499
views
GATK4 haplotypecaller calls variants on regions without read coverage
GATK4 CNNScoreVariants haplotypecaller
13 days ago by thomas.heigl.ibk • 0
3
votes
6
replies
527
views
normalization in single cell
normalization scRNA-seq single-cell
updated 18 days ago by 5.5k • written 20 days ago by ▴ 20
5
votes
6
replies
544
views
Download files from Experiment Acession
BioProject NCBI SRA
16 days ago by Manuel Sokolov Ravasqueira ▴ 110
4
votes
6
replies
483
views
Batch correction preserving biological difference
scRNA-Seq batch-correction
10 days ago by foejvs546 ▴ 20
5
votes
6
replies
751
views
Uploading HiC track on UCSC browser
custom_track UCSC HiC
updated 26 days ago by ★ 1.7k • written 6 months ago by ▴ 50
1
vote
6
replies
469
views
Last against ncbi nr database
metagenomics virus alignment
20 days ago by Md Moinuddin • 0
1
vote
6
replies
567
views
Need to split a cram file into smaller pieces - how to extract and save cram format to a new file?
samtools CRAM
updated 20 days ago by ★ 1.3k • written 4 weeks ago by ★ 2.4k
1
vote
6
replies
1.1k
views
ROSE called super-enhancers overlapping with promoters
super-enhancers ROSE ChIP-seq
updated 18 days ago by ★ 17k • written 7 months ago by ▴ 10
2
votes
6
replies
402
views
How to convert .sdf files into .sdf.gz?
file-conversion
22 days ago by Sanjukta • 0
12
votes
6
replies
737
views
Downloading paired end fastq data from SRA
SRA single-cell RNA-Seq
11 days ago by Matheus • 0
4
votes
6
replies
448
views
Python for pdf reports
Cancer Python3 reports
updated 9 days ago by ▴ 100 • written 11 days ago by ▴ 10
3
votes
6
replies
504
views
how to effectively pipe chromap into samtools view
samtools bash pipe
26 days ago by Matteo Ungaro ▴ 100
8
votes
6
replies
501
views
Non-existent transcript as a result from Salmon
RNAseq salmon
14 days ago by Vojtěch ▴ 10
4
votes
6
replies
527
views
gene naming
gene-names ensembl blast
updated 5 days ago by 145k • written 24 days ago by ▴ 10
3
votes
6
replies
487
views
RNA seq mapping
RNA-seq
updated 24 days ago by 44k • written 5 weeks ago by • 0
4
votes
6
replies
542
views
advice for visualizing a graph genome constructed by "vg construct"
vg
29 days ago by Jong ▴ 10
2
votes
6
replies
1.5k
views
Batch effect that is same as main factor
batch-effect RNA-Seq
updated 16 days ago by 44k • written 2.9 years ago by ▴ 70
0
votes
6
replies
1.6k
views
How to Convert Illumina Final Report File To Plink
Illumina plink
updated 7 days ago by • 0 • written 14 months ago by • 0
12
votes
6
replies
7.6k
views
Download Hg18 Snp Database
snp
updated 15 days ago by ★ 4.3k • written 13.4 years ago by ▴ 140
3
votes
6
replies
604
views
Why Can’t I Find the URL and Details for I-Mutant3.0? Does It Even Exist? Urgent Help Needed from Experts!”
I-mutant
17 days ago by 半桶 • 0
4
votes
6
replies
1.1k
views
Aligning reads from mouse samples that express 1 human gene
realignment
updated 24 days ago by 14k • written 22 months ago by ▴ 160
6
votes
6
replies
754
views
If changing the RNA-Seq count normalisation method changes the DGE and downstream analysis results?
tpm normalisation fpm
5 days ago by analyst ▴ 50
5
votes
6
replies
527
views
How do I find allele frequencies from GATK output?
allele-frequency GATK muller-plot
3 days ago by mgranada3 ▴ 40
3
votes
6
replies
511
views
which bed file should be used for deeptools computeMatrix
atac-seq deeptools
updated 29 days ago by ★ 4.3k • written 4 weeks ago by ▴ 60
1
vote
6
replies
522
views
Analyzing PCA Clustering from PLINK Output
plink
13 days ago by Smriti ▴ 30
0
votes
6
replies
582
views
Associate Roary output with locus_tag from specific genome
bacteria locus_tags genomics
updated 19 days ago by 21k • written 7 weeks ago by • 0
565 results • Page 2 of 12
Recent Votes
How to identify temporal differential gene expression patterns among cell types in scRNA-seq
Comment: How can I get the list of all human ensembl transcript ids?
Answer: How can I get the list of all human ensembl transcript ids?
What Are The Most Common Stupid Mistakes In Bioinformatics?
What Are The Most Common Stupid Mistakes In Bioinformatics?
Answer: Mate pairs and paired reads confusion
p value of significance for overlapping peaks
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Recent Replies
Answer: Quality check pipeline for PCR cDNA ONT sequencing output. by GenoMax 145k
ONT provides a workflow for working with transcriptomic data: https://github.com/epi2me-labs/wf-transcriptomes Assuming `dorado` has been …
Comment: Trimmomatic or Cutadapt not Trimming my Adapters even though I see them clearly by GenoMax 145k
Your file appears to be in correct multi-fasta format. Please check out two other popular options that have easy to understand options. …
Comment: Freelance Bioinformatician Required by BioinfGuru ★ 2.1k
Please include a professional link of your own. It is truly unprofessional to request data like this without verification. You are complete…
Answer: Trimmomatic or Cutadapt not Trimming my Adapters even though I see them clearly by BioinfGuru ★ 2.1k
I am assuming you have included -o and -p options for paired end sequencing. You should always post the full command you use. Your partia…
Comment: Trimmomatic or Cutadapt not Trimming my Adapters even though I see them clearly by obsto123 • 0
sorry for the weird syntax of the contents of the "contam_file.fa". It is in the correct format, somehow while copy-pasting it got transfer…
Comment: How to generate sequence length distribution from Fasta file by xiaoleiusc ▴ 140
Just found that `cat file.fa | awk '$0 ~ ">" {print c;c=0} $0 !~ ">" {c+=length($0);} END { print c; }' | sed '/^$/d' | sort | uniq -c | aw…
Comment: How to generate sequence length distribution from Fasta file by xiaoleiusc ▴ 140
Thanks, Nick, if I want to output a .tsv format table with tab-delimited length and count, how should I modify your command line?
Comment: Structural alignment of protein by Sadik Muzemil ▴ 20
Thanks a lot @mensur exactly what I am looking for. I will look into the [paper][1] for details. [1]: https://doi.org/10.1038/s41587-0…
Answer: p value of significance for overlapping peaks by i.sudbery 20k
We use the [GAT][1] tool for this. I believe there is an R package that does something similar (shuffles one set of peaks and then compares…
Answer: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do? by Randy H ▴ 110
Odd. WGS Extract provides the buttons for sorting and indexing once a file is opened (if it is not already sorted and/or indexed). BUT, a C…
Answer: Freelance Bioinformatician Required by 飞走的纸飞机 • 0
Hi, I am interested in the analysis of metagenomes,I am familiar with biological workflow building using nextflow, I am also familiar with …
Comment: CombatSeq introduces clustering in RNA-seq data (miRNA) by Michael 55k
Could you add "sex" as a covariate to the plot?
Comment: How does the DNA-seq machine know which strand that is forward/reverse? by scchess ▴ 640
Alignment file would have the strand information
Comment: Help Needed: Importing and Analyzing GWAS Data from GWAS Catalog in R by 1769mkc ★ 1.2k
show some part of your data using `dput(head(df))` that would be helpful for anyone who can give you help
Comment: FastTree error: Non-unique name 'xxxxx' in the alignment by eedeaguiar • 0
Ah okay good to know, thank you for your response. To clarify, I don't have 4+1 sequences, I have 34,000 sequences. I will look into this f…
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