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768 results • Page 3 of 16
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2
votes
6
replies
522
views
Genotypes in vcf files
genotypes vcf
updated 16 days ago by 22k • written 16 days ago by ▴ 160
7
votes
6
replies
1.1k
views
How does 10x Genomics 3' single cell data have reads aligning to exons that aren't terminal?
single-nucleus rna-seq igv single-cell
updated 20 days ago by 41k • written 9 months ago by ▴ 40
1
vote
6
replies
555
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4 bwa-mem target-capture-sequencing alignment
18 days ago by Miguel • 0
1
vote
6
replies
535
views
frequency plot for peaks
chip-seq chipseeker
updated 12 days ago by ▴ 400 • written 27 days ago by ▴ 10
14
votes
6
replies
6.0k
views
What Tool Should I Use To Assemble Data Produced By A 454 Sequencer?
assembly next-gen-sequencing
updated 27 days ago by 41k • written 13.6 years ago by ▴ 80
30
votes
6
replies
13k
views
What Are Some Good Free Bioinformatics And Computational Biology Books?
books online
updated 27 days ago by 41k • written 13.6 years ago by ★ 1.0k
0
votes
6
replies
404
views
Resolving over clustered NGS with Q-scores
NGS phred Q-score overclustering
4 days ago by sam.himes92 • 0
2
votes
6
replies
450
views
Filter a BED file based on genome coordinates for gene names
BED GTF GFF
updated 27 days ago by 41k • written 28 days ago by • 0
2
votes
6
replies
6.9k
views
Extracting chimeric reads from mapping
RNA-Seq alignment samtools bwa
updated 11 days ago by • 0 • written 6.2 years ago by ▴ 20
0
votes
6
replies
415
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq Nanopore ONT differential expression
11 days ago by tw_140 • 0
3
votes
6
replies
496
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq cells mRNA expression gene
updated 9 days ago by ★ 1.3k • written 11 days ago by ▴ 40
4
votes
6
replies
2.0k
views
How to do simple pathway analysis?
rna-seq genome gene
updated 3 days ago by • 0 • written 4.6 years ago by ▴ 110
2
votes
6
replies
323
views
Multi-factor designs in DiffBind
Chipseq Multi-factor Diffbind
updated 3 days ago by ★ 2.0k • written 4 days ago by • 0
2
votes
6
replies
2.1k
views
No best K value found
Assembly Kmergenie
updated 16 days ago by • 0 • written 6.8 years ago by ▴ 80
2
votes
6
replies
707
views
need interpretations for the vg call output
vcf vg
22 days ago by Maxine ▴ 40
1
vote
6
replies
401
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
12 days ago by CTLong ▴ 50
0
votes
6
replies
329
views
I made an error when using metawrap to binning
metagenome binning metawrap
13 days ago by alice005201314 • 0
0
votes
6
replies
556
views
Help locating TCGA data from cbioportal
cancer TCGA RNA cbioportal CNA
26 days ago by ConvolutedGenome ▴ 20
2
votes
6
replies
557
views
6 follow
STAR ALIGNMENT
alignment-rate
updated 4 days ago by • 0 • written 23 days ago by ▴ 20
2
votes
6
replies
409
views
Quality filtering prior to pseudoalignment
fastp rna-seq pseudoalignment kallisto
updated 25 days ago by 20k • written 26 days ago by ▴ 20
10
votes
6
replies
4.9k
views
How to create interval list from reference fasta or dict file?
GATK
updated 1 day ago by ▴ 100 • written 2.9 years ago by ★ 1.3k
13
votes
6
replies
9.1k
views
What To Do With An Error In The Fastq Illumina Quality Scores
fastx-toolkit next-gen-sequencing fastq
updated 27 days ago by 41k • written 13.7 years ago by ★ 1.3k
4
votes
6
replies
491
views
how to count the number of reads align per viruses in my sample
RNAseq samtools illumina
updated 25 days ago by 136k • written 27 days ago by • 0
2
votes
6
replies
478
views
Burrows-Wheeler transform
Python BWT DNA
updated 27 days ago by 41k • written 28 days ago by • 0
6
votes
6
replies
461
views
6 follow
How to align a genome fasta file from NCBI to a reference genome?
genome genetics alignment
updated 18 days ago by ★ 5.1k • written 19 days ago by • 0
4
votes
6
replies
412
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
20 days ago by Tihana ▴ 10
12
votes
6
replies
497
views
Problematic fastq files...How can we trust them?
fastq
9 days ago by blackadder ▴ 30
13
votes
6
replies
378
views
6 follow
how to sort fasta file according to a header file
fasta
updated 19 days ago by 41k • written 19 days ago by ▴ 20
5
votes
6
replies
467
views
Generate Read counts from bam file
RNAseq reference_genome Deseq2 read_counts
updated 11 days ago by ▴ 10 • written 12 days ago by • 0
6
votes
6
replies
448
views
6 follow
STAR alignment speed
STAR alignment RNA
updated 19 days ago by 78k • written 20 days ago by • 0
4
votes
6
replies
487
views
From TPM to raw counts
tpm Deconvolution rnaseq
8 days ago by Gama313 ▴ 120
4
votes
6
replies
2.9k
views
Gene Similarity Search
conservation similarity
updated 27 days ago by 41k • written 13.7 years ago by ▴ 790
0
votes
6
replies
1.7k
views
DiffBind dba.analyze never finishes
ChIP-Seq R DiffBind FAIRE-seq DESeq2
updated 23 days ago by ★ 2.0k • written 2.9 years ago by • 0
2
votes
6
replies
335
views
gatk SelectVariants is giving duplicate allele error while extracting SNPs out of vcf file
SNP variant-calling gatk
updated 2 days ago by 41k • written 3 days ago by ▴ 10
4
votes
6
replies
483
views
bwa mem hangs after a few thousand reads
bwa-mem alignment bwa calling variant
11 days ago by cee28 ▴ 30
4
votes
6
replies
598
views
BLAST hits on viruses relate to different host than used
Phage BLAST Metagenomics
15 days ago by DonPhager • 0
0
votes
6
replies
573
views
Add braces to the DNA sequence for re quested primer position.
python subprocess
updated 25 days ago by 41k • written 4 weeks ago by • 0
2
votes
6
replies
416
views
which statistical test and which package for comapre datasets?
R package statistical test
updated 4 hours ago by 3.8k • written 1 day ago by • 0
11
votes
6
replies
739
views
6 follow
UMAP or TSNE for single cells?
single-cell
updated 17 days ago by ▴ 40 • written 24 days ago by ▴ 80
1
vote
5
replies
671
views
ATAC-Seq and RPKM
RPKM ATAC-Seq
updated 5 days ago by 78k • written 9 weeks ago by • 0
6
votes
5
replies
410
views
Calculate GC content for entire chromosome
bam GC assembly bwa-mem
updated 4 days ago by 5.8k • written 5 days ago by • 0
1
vote
5
replies
1.5k
views
BLAST: overflow error
BLAST
updated 7 days ago by 136k • written 19 months ago by ▴ 60
5
votes
5
replies
1.8k
views
GSEA for RNA_seq dataset
DEGs GSEA RNA-seq
updated 5 days ago by 41k • written 2.7 years ago by ▴ 20
1
vote
5
replies
336
views
vcftools
vcftools
updated 6 days ago by ▴ 10 • written 6 days ago by • 0
1
vote
5
replies
345
views
bcftools mipileup error: format error, unexpected A at line 1
bcftools
updated 27 days ago by ▴ 520 • written 27 days ago by ▴ 20
0
votes
5
replies
566
views
Lack of correspondance of GFA node IDs to giraffe/call node IDs
giraffe pggb vg
updated 13 days ago by • 0 • written 7 weeks ago by • 0
13
votes
5
replies
6.8k
views
How To Align Reads Obtained From Sequence Capture
exome-sequencing next-gen-sequencing sequence
updated 27 days ago by 41k • written 13.7 years ago by 99k
1
vote
5
replies
383
views
How can I map coordinates between two strains of yeast?
coordinates yeast genome mapping fasta
10 days ago by Jimmy ▴ 10
0
votes
5
replies
300
views
GetPileupSummaries intervals-list with Targeted Sequencing?
Variant-Calling Somatic intervals.bed GetPileUpSummaries GATK
updated 1 day ago by 158k • written 1 day ago by ▴ 100
7
votes
5
replies
1.4k
views
How to learn Scanpy
scanpy Python rna-seq
updated 17 days ago by ★ 2.7k • written 17 months ago by ▴ 30
768 results • Page 3 of 16
Recent Votes
Answer: Converting a .frq file to a data frame?
Answer: Multi-factor designs in DiffBind
Answer: How to speed-up to contruct phylogenetic tree
Comment: How to speed-up to contruct phylogenetic tree
Answer: Renaming fasta files with their headers
Comment: What apps can read large FASTQ files on Windows?
Answer: Renaming fasta files with their headers
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Recent Replies
Comment: bcftools=1.18 not filtering correcting MAF by raphael.B ▴ 470
Hello, Is `MAF` flag defined in your VCF?
Comment: Converting a .frq file to a data frame? by colindaven 5.8k
Also get rid of the curly braces in the col5 header `{}`
Answer: How to speed-up to contruct phylogenetic tree by Michael 53k
I agree with the other recommendations and I wouldn't recommend MEGA either, but would like to add that most programs, including MEGA, have…
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Yes, Its perfectly working.. It will be useful if you share concat command too if there are same genes in the fasta file Thank you
Answer: Renaming fasta files with their headers by shenwei356 8.3k
I've got a general method, but you need to have some basic knowledge of regular expressions. If not, please learn them for 30 minutes: -…
Comment: Renaming fasta files with their headers by liorglic ★ 1.3k
It's hard to understand what your input and desired output look like. Please edit your original question so it includes a clear explanation…
Comment: SRA toolkit (NCBI) - sra to fasta by ATpoint 78k
Can be 23 or 109, it does not matter.
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Thank you for your code, but i have a fasta file which contains [gene=rps12] ids, so i want to rename the header with gene id alone like >r…
Answer: How to speed-up to contruct phylogenetic tree by Mensur Dlakic ★ 25k
It depends on how long your protein is. Generally speaking, it shouldn't take weeks or months. Trees with more than ~100 branches are very …
Comment: How to speed-up to contruct phylogenetic tree by liorglic ★ 1.3k
Is there a specific reason you need to use MEGA? Maybe try another software which might be faster (e.g. PhyML, RaxML, IQ-TREE). Also, do yo…
Answer: Renaming fasta files with their headers by liorglic ★ 1.3k
Assuming that you have a directory containing multiple files with `.fasta` extension, each containing one record, you can do something like…
Comment: What are the methods to correlate/study metabolomics data to proteomics data? by LauferVA 3.8k
thank you, @wuschel, for the comprehensive reply.
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
i tried this command awk -F 'gene=|]|[.]{1}' '/^>/ {print $2}' 7seqNC_018552.1cds.fasta > 7NC_018552.fasta got only gene name alone wit…
Answer: Converting a .frq file to a data frame? by zau saa ▴ 80
simply add a word to line 1 as the name of column 6
Comment: SRA toolkit (NCBI) - sra to fasta by Sanjukta • 0
Hi there, will it be an issue if we do not mention 60?
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