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1,000 results • Page 4 of 20
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9
votes
6
replies
3.1k
views
Bug in JellyFish and DSK k-mer counting tool?
dsk jellyfish k-mer
7.5 years ago by scchess ▴ 640
9
votes
5
replies
1.2k
views
how to retrieve all proteins related to cancer
proteins
8.0 years ago by Learner ▴ 280
9
votes
13
replies
3.4k
views
Python Script to map reads to reference sequence
sequence python mapping script reference sequence
5.1 years ago by Fid_o ▴ 40
9
votes
7
replies
3.3k
views
Aligning Miseq With Deletions >10 Bases
alignment miseq next-gen
updated 10.8 years ago by 20 • written 11.3 years ago by 4.2k
9
votes
13
replies
1.6k
views
SNP's and Gene?
SNP gene
4.6 years ago by imgapgenomika ▴ 10
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.8 years ago by 15k • written 3.8 years ago by ▴ 160
9
votes
7
replies
5.4k
views
How to combine a different sources of pathway database (KEGG, BioCarta) for Pathway analysis.
Pathway enrichment analysis GWAS pathway analysis
7.9 years ago by kmsh410 ▴ 40
9
votes
10
replies
2.8k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK Whole Exome Sequencing Mutect2
3.3 years ago by kwanghoon ▴ 20
9
votes
5
replies
3.9k
views
What's the interpretation behind Pathway enrichment analysis
networks pathway enrichment analysis gene
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 260
9
votes
12
replies
1.5k
views
Copy number variations analysis
R CNV
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 70
9
votes
4
replies
5.6k
views
How to analyse normalized read count?
RNA-Seq R
updated 16 months ago by 43k • written 8.9 years ago by ▴ 150
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R gene sequence SNP
5.5 years ago by bioinfo456 ▴ 150
9
votes
19
replies
2.4k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.3 years ago by schlogl ▴ 160
9
votes
6
replies
1.9k
views
Question about featureCounts
RNA-Seq featurecounts
updated 2.8 years ago by • 0 • written 4.6 years ago by ▴ 30
9
votes
10
replies
2.5k
views
why there is 0/0 genotyp in VCF file?
VCF GATK Variant
4.8 years ago by star ▴ 350
9
votes
7
replies
1.3k
views
Reference genome location
reference positions FASTA alignment genome
updated 16 months ago by ★ 2.1k • written 16 months ago by • 0
9
votes
2
replies
3.1k
views
GEOquery Problems to Get GEO dataset
Geoquery
8.1 years ago by Shicheng Guo ★ 9.4k
9
votes
11
replies
1.5k
views
6 follow
Split up excel cell into multiple records
excel byonic
6.8 years ago by rshipman ▴ 30
9
votes
2
replies
593
views
Answer needed urgently
Deep
updated 20 months ago by ★ 27k • written 20 months ago by • 0
9
votes
5
replies
3.8k
views
Which bias flags to run with Salmon before DESeq2 analysis?
RNA-Seq Salmon DESeq2 Bias Flags
4.9 years ago by cameron.holman ▴ 20
9
votes
11
replies
4.5k
views
please someone help me with running mirdeep2
software error mirdeep2 perl
7.6 years ago by zizigolu ★ 4.3k
9
votes
14
replies
4.4k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 70
9
votes
7
replies
2.8k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression differential average R rna-seq
updated 2.8 years ago by ▴ 60 • written 2.9 years ago by ▴ 250
9
votes
5
replies
5.3k
views
Binning of reads vs. binning of contigs in metagenomics
Binning Metagenomics
5.5 years ago by vijinim ▴ 100
9
votes
1
reply
6.1k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq macs macs2
updated 20 months ago by 43k • written 8.6 years ago by ★ 3.4k
9
votes
13
replies
2.4k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 30
8
votes
9
replies
1.5k
views
6 follow
Featurecount is 0 while TPM is 6289.54
TPM Count Feature
2.4 years ago by zhangmeng21 ▴ 10
8
votes
7
replies
1.6k
views
Splitting the overall RNA-seq data
RNA-Seq
6.9 years ago by aeserrano ▴ 40
8
votes
14
replies
2.5k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
2.8 years ago by johnsonqinz • 0
8
votes
14
replies
6.0k
views
Error in BWA-MEM running in linux
RNA-Seq BWA-MEM alignment
updated 6.0 years ago by 142k • written 6.0 years ago by ▴ 170
8
votes
11
replies
5.0k
views
Increasing kmer limit in SPAdes
Assembly Bacterial Spades Velvet
7.8 years ago by rrcutler ▴ 120
8
votes
4
replies
870
views
Correlation network analysis
rna-seq
3.4 years ago by Lepomis_8 ▴ 30
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 5.7 years ago by 43k • written 8.2 years ago by ▴ 50
8
votes
11
replies
2.7k
views
directionality of RRBS
directional non-directional RRBS
updated 2.8 years ago by ★ 2.9k • written 2.9 years ago by ▴ 140
8
votes
3
replies
5.3k
views
Bioinformatics project for a beginner
projects
updated 22 months ago by 43k • written 8.4 years ago by ▴ 30
8
votes
6
replies
1.3k
views
How to apply bioinformatic in vaccine design?
Vaccine
updated 18 months ago by ★ 2.5k • written 18 months ago by ▴ 50
8
votes
7
replies
1.3k
views
grep with -f switch is not working
grep
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 30
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
8
votes
13
replies
1.7k
views
Mapped reads not mapping to a real sequence?
bam sam samtools kallisto
15 months ago by txema.heredia ▴ 110
8
votes
5
replies
1.1k
views
Bioinformatics Definitions
genome
updated 2.9 years ago by ★ 2.5k • written 2.9 years ago by ▴ 40
8
votes
14
replies
2.4k
views
6 follow
Definition of "=" in comparing two genes
sequencing gene
updated 2.5 years ago by 43k • written 9.9 years ago by • 0
8
votes
8
replies
1.6k
views
Clustering DNA sequences (from human genome)
sequencing genome
4.7 years ago by abdul.karim • 0
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
6.3 years ago by Sharon ▴ 610
8
votes
1
reply
8.6k
views
Correlation heatmaps: use correlation as clustering distance or not?
heatmap RNA-Seq clustering
5.1 years ago by CuriousGuy ▴ 90
8
votes
3
replies
856
views
How safe the UCSC is for patients data
RNA-Seq
updated 4.7 years ago by 82k • written 4.7 years ago by ▴ 240
8
votes
1
reply
1.6k
views
Genome Sequencing And Evolutionary History
evolution
updated 10.3 years ago by 49k • written 10.3 years ago by ▴ 110
8
votes
8
replies
2.5k
views
6 follow
Blast Is Giving Me A Result Totally Unrelated To The Gene I Expect
blast primer
updated 10.9 years ago by 20 • written 11.1 years ago by • 0
8
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
11 months ago by yoshifumimiya ▴ 40
8
votes
30
replies
5.2k
views
Per Base Sequence Content
sequencing fastqc genome sequence
updated 4.1 years ago by ▴ 560 • written 4.1 years ago by ▴ 20
8
votes
6
replies
2.6k
views
for low coverage RNAseq how many reads assigned is the bare minimum for differential gene expression analysis
RNA-Seq
5.3 years ago by senowinski ▴ 30
1,000 results • Page 4 of 20
Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
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Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p by ATpoint 82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis by Jacek ▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap by dariober 14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by melissa.joubert • 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data? by Arton • 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax? by mbrav005 • 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon by sansan_96 ▴ 90
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