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1,000 results • Page 3 of 20
Sort: Votes
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5
votes
2
replies
485
views
30 bp sequence that does not show hit within a genome
similarity
updated 9 months ago by 8.2k • written 9 months ago by ▴ 400
5
votes
6
replies
701
views
error: Couldn't open trackDb.txt in hubCheck
UCSC hubCheck
updated 10 months ago by 11k • written 10 months ago by ▴ 320
5
votes
6
replies
3.1k
views
Can't access DAVID
DAVID
updated 9 months ago by 40k • written 8.3 years ago by ★ 4.1k
5
votes
5
replies
439
views
Convert genomic files from known Gigabases(# of bases) to gigabytes
gigabases gigabytes genomics
updated 7 months ago by 135k • written 7 months ago by ▴ 520
5
votes
1
reply
315
views
Enricher with Gene Symbols
DGE ClusterProfiler Enrich ORA
updated 7 weeks ago by ★ 1.4k • written 7 weeks ago by ▴ 100
5
votes
11
replies
575
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 8 weeks ago by 40k • written 8 weeks ago by ▴ 200
5
votes
7
replies
1.1k
views
error while using cyvcf2 to parse the vcf file
cyvcf2 vcf htslib
updated 4 months ago by 40k • written 16 months ago by ▴ 140
5
votes
3
replies
878
views
abyss-pe genome assembly
konnector abyss-pe
updated 3 months ago by 40k • written 4.7 years ago by • 0
5
votes
6
replies
1.9k
views
check duplicates in two columns
ChIP-Seq sequencing SNP
updated 9 months ago by 40k • written 8.3 years ago by • 0
5
votes
8
replies
1.7k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 10 weeks ago by ▴ 360 • written 8 months ago by • 0
5
votes
4
replies
3.4k
views
gender SNP marker
SNP
updated 10 months ago by 40k • written 8.2 years ago by • 0
5
votes
6
replies
1.2k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools bam bed
updated 3 months ago by 40k • written 11 months ago by ▴ 350
5
votes
9
replies
3.7k
views
Combining all biological replicates
RNA-Seq Cuffdiff
updated 11 months ago by 40k • written 8.2 years ago by ▴ 10
5
votes
7
replies
758
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 4 months ago by • 0 • written 3.8 years ago by ▴ 50
5
votes
4
replies
1.8k
views
MyVariant.info fields descriptions?
genome snp variant
updated 6 months ago by 40k • written 7.4 years ago by ▴ 90
5
votes
6
replies
884
views
I can not allocate ram memory for WSL2
WSL2
6 months ago by ailton • 0
5
votes
10
replies
607
views
Error when viewing a bam file
samtools
updated 3 months ago by 40k • written 5 months ago by ▴ 200
5
votes
2
replies
660
views
how to loop through various dataframes in R
dataframe R
updated 9 months ago by 11k • written 9 months ago by ▴ 140
5
votes
5
replies
3.4k
views
Gencode annotation and read counting- how to handle overlapping/ambiguous features
gencode alignment RNA-Seq
updated 9 months ago by 40k • written 8.3 years ago by ▴ 680
5
votes
6
replies
1.2k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2 R RNA-Seq
updated 3 months ago by 40k • written 3.4 years ago by ▴ 80
5
votes
6
replies
532
views
normalize coordinates to the same length
r genomicranges
6 months ago by Chironex ▴ 40
5
votes
10
replies
793
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR RNA-seq
5 weeks ago by alwayshope ▴ 30
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection DE-genes multi-treatments time-series
updated 4 months ago by 40k • written 7.2 years ago by ▴ 740
5
votes
2
replies
2.9k
views
Cut & run - bowtie2 dovetail option
cut and run dovetail bowtie2
updated 8 months ago by • 0 • written 2.9 years ago by ▴ 280
5
votes
35
replies
2.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome vg
updated 12 weeks ago by ▴ 360 • written 3 months ago by • 0
5
votes
3
replies
580
views
GENE code ID conversion
ensembl entrez
6 months ago by Confused_human ▴ 10
5
votes
4
replies
853
views
Converting Bam file to Fasta (Zipped)
bedtools samtools
updated 3 months ago by 40k • written 11 months ago by ▴ 350
5
votes
7
replies
2.6k
views
download recent list of human exons
human-exons
updated 11 months ago by 40k • written 8.2 years ago by ▴ 20
5
votes
12
replies
892
views
Data from an experiment
single-cell
updated 7 months ago by 135k • written 7 months ago by ▴ 200
5
votes
7
replies
544
views
About the value in bigwig file
ATAC-seq
updated 12 weeks ago by ▴ 840 • written 3 months ago by ▴ 200
5
votes
8
replies
1.1k
views
snpeff install error
snpeff
updated 4 months ago by 40k • written 5 months ago by ▴ 20
5
votes
4
replies
947
views
Running nf-core rnaseq with smart-seq3 data
smart-seq3 nf-core nextflow
10 months ago by firestar ★ 1.6k
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods research gene
updated 4 months ago by 40k • written 5.7 years ago by • 0
5
votes
9
replies
2.6k
views
differential expression analysis tools for single end reads
rna-seq next-gen
updated 11 months ago by 40k • written 8.2 years ago by ▴ 90
4
votes
7
replies
2.4k
views
low bootstrap value?
phylogeny genome alignment
updated 4 months ago by 40k • written 4.3 years ago by ▴ 120
4
votes
5
replies
461
views
STAR mapping - regarding output files content
STAR RNA-seq mapping
updated 6 weeks ago by ▴ 840 • written 7 weeks ago by • 0
4
votes
11
replies
944
views
PCA WITH PLINK
PLINK
updated 6 weeks ago by 86k • written 7 weeks ago by • 0
4
votes
7
replies
2.5k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 6 months ago by 40k • written 2.3 years ago by ▴ 70
4
votes
7
replies
1.0k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 10 weeks ago by 135k • written 10 weeks ago by • 0
4
votes
2
replies
2.0k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 3 months ago by 40k • written 10.7 years ago by ▴ 50
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 4 months ago by 40k • written 6.3 years ago by ▴ 730
4
votes
2
replies
453
views
Analyzing bulk RNA-seq
RNAseq
updated 8 months ago by 13k • written 8 months ago by • 0
4
votes
8
replies
868
views
Is possible to run VEP without consequence calculation?
vep annotation
11 months ago by magnolia ▴ 20
4
votes
3
replies
553
views
Is there a possibility of Cd45- immune cells in single cell-rna seq?
single-cell immune-cells scRNA-seq
9 months ago by eaglesfeet ▴ 20
4
votes
5
replies
3.0k
views
WGCNA TOM calculation time
RNA-Seq R WGCNA
7 months ago by tothepoint ▴ 770
4
votes
3
replies
574
views
Testing overlap significance of three gene sets using the hypergeometric distribution
Hypergeometric-distribution gene-sets
5 months ago by Pac314 ▴ 10
4
votes
5
replies
313
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 7 weeks ago by 135k • written 8 weeks ago by • 0
4
votes
3
replies
2.8k
views
INDEL and point mutation at same position in VCF
vcf alignment indels snps
updated 9 months ago by 40k • written 8.3 years ago by ▴ 20
4
votes
6
replies
932
views
Transcript quantification
rna-seq transcriptome SRA
updated 3 months ago by 77k • written 3 months ago by • 0
4
votes
4
replies
343
views
Request for a linkage analysis tutorial
linkage
updated 7 weeks ago by 135k • written 7 weeks ago by ★ 2.9k
1,000 results • Page 3 of 20
Recent Votes
Answer: tensorQTL interaction issue
Answer: Script for getting summary statistic of any genome using GTF or GFF3 ?
Comment: How do you validate and verify your pipeline's software updates?
Comment: How do you validate and verify your pipeline's software updates?
Answer: GSEA with GO and KEGG datasets
GSEA with GO and KEGG datasets
Answer: Exporting DEGs obtained from DESeq2
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Recent Replies
Comment: How to get sample names and genotype for SNP in multi-sample VCF file by Kevin Blighe 86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF by alejandrogzi ▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF by alejandrogzi ▴ 30
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other by alejandrogzi ▴ 30
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
Answer: How Do I Convert From Bed Format To Gff Format? by alejandrogzi ▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue by Solal • 0
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners. by Qboy • 0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by langziv ▴ 50
Thanks. I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file by avelarbio46 ▴ 30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by GenoMax 135k
> so I don't think the genome size is available. Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output by 睿紘 • 0
For additional information, "Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by langziv ▴ 50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by langziv ▴ 50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929. I just rem…
Comment: Understanding mother and father alleles in VCF file by c. • 0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by GenoMax 135k
Correct. Data that went into the assembly.
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