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121,961 results • Page 183 of 2440
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0
votes
7
replies
1.6k
views
SNP calling with many samples using bcftools
bcftools SNP multithreading
22 months ago by George ▴ 20
4
votes
6
replies
2.5k
views
Handling multiple fastq files per sample, per lane, per read out of the Cellranger bam to fastq workflow
bamtofastq cellranger RNA-seq
22 months ago by Erfanesi • 0
0
votes
0
replies
468
views
Combining SNP array data from different chip versions
Array Illumina SNP GWAS
22 months ago by Marlene • 0
1
vote
2
replies
1.2k
views
set GT values to missing in VCF file for specific sample-variant combinations - bcftools?
bcftools missing GT vcf
22 months ago by karen2 • 0
0
votes
0
replies
535
views
Getting message while running generateMap.pl from hmmcopy_utils
cnv linux mappability hmmcopy_utils
22 months ago by kabir.deb ▴ 90
0
votes
1
reply
1.0k
views
Error in H5Fopen
atac-seq scatac-seq
updated 22 months ago by • 0 • written 3.3 years ago by ▴ 30
3
votes
2
replies
914
views
Compare similarity of protein variants
protein structure
updated 22 months ago by ★ 3.1k • written 22 months ago by ▴ 10
0
votes
1
reply
1.2k
views
Trimming pair end fastq files merged not interleaved
pair end trimming merged
updated 22 months ago by 20k • written 22 months ago by ▴ 100
2
votes
4
replies
1.3k
views
[main_samview] fail to read the header from "human_g1k_v37.annotate.fasta".
reference samtools fasta
updated 22 months ago by ★ 1.3k • written 22 months ago by • 0
2
votes
2
replies
962
views
Splice junction SNPs
SNP splicing isoform
updated 22 months ago by 23k • written 22 months ago by ▴ 420
0
votes
2
replies
723
views
Bcftools
bcftools vcf
updated 22 months ago by 45k • written 22 months ago by • 0
1
vote
3
replies
1.0k
views
DNA/RNA Sequence Alignment
dna rna alignment sequence
updated 22 months ago by ★ 30k • written 22 months ago by • 0
5
votes
5
replies
1.5k
views
salmon for gene expression quantification
salmon gene-expression
updated 22 months ago by ★ 7.7k • written 22 months ago by • 0
0
votes
1
reply
1.1k
views
how to create a consensus sequence from different assemblies
consensus sequence
updated 22 months ago by 20k • written 22 months ago by ▴ 10
0
votes
2
replies
768
views
hisat2-build
hisat2-build hisat2
22 months ago by Bjorn • 0
2
votes
6
replies
2.0k
views
Quality filtering prior to pseudoalignment
fastp rna-seq pseudoalignment kallisto
updated 22 months ago by 20k • written 22 months ago by ▴ 20
0
votes
0
replies
410
views
ChIPQC object creation is throwing error
ChipQC
22 months ago by mavy ▴ 10
0
votes
1
reply
741
views
DESeq2 with unbalanced dataset and multifactor design
DESeq2
updated 22 months ago by ★ 1.9k • written 22 months ago by • 0
0
votes
3
replies
7.0k
views
Parsing Pdb file using Biopython parser: How to get all atoms instead of duplicates?
sequence software error assembly biopython
updated 22 months ago by ▴ 20 • written 6.1 years ago by • 0
0
votes
2
replies
1.3k
views
Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
samtools bwa
updated 22 months ago by ★ 1.3k • written 22 months ago by ▴ 10
1
vote
3
replies
1.3k
views
Clumping with r2=0 and 250kb radius in plink
plink clump
22 months ago by landscape95 ▴ 190
0
votes
4
replies
1.4k
views
Query regarding callsets used as known sites in Variant Calling
GATK VCF
22 months ago by Shruti Baikerikar • 0
0
votes
3
replies
987
views
accessing the gene on fastq data
rna-seq sra
updated 22 months ago by 4.7k • written 22 months ago by • 0
1
vote
9
replies
1.7k
views
Htseq-count reads with missing mate encountered
htseq htseq-count
22 months ago by Bjorn • 0
0
votes
2
replies
797
views
Doubt about RNASeq Paired-end process
RNASEQ NGS Paired-end
22 months ago by Vicent • 0
13
votes
21
replies
3.6k
views
Practical Haplotype Graph Paths
practical-haplotype-graph PHG
updated 20 months ago by ▴ 220 • written 22 months ago by ▴ 10
0
votes
2
replies
741
views
standalone blastx of queries without NR annotations
miRNA lncRNA
22 months ago by analyst ▴ 70
1
vote
2
replies
1.2k
views
ComBat-seq problem
ComBat-seq RNA-Seq batch-effect
updated 22 months ago by 45k • written 22 months ago by ▴ 60
0
votes
2
replies
1.6k
views
AlphaMissense_hg38.tsv.gz tabix indexing issue VEP
Plugin VEP AlphaMissence
22 months ago by Katsiaryna • 0
4
votes
6
replies
1.4k
views
how to count the number of reads align per viruses in my sample
RNAseq samtools illumina
updated 22 months ago by 154k • written 22 months ago by • 0
2
votes
8
replies
2.6k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
22 months ago by nick_b55 ▴ 20
1
vote
2
replies
734
views
Extract individual samples from combined gvcf file
GATK CombineGVCFs
22 months ago by Shin Taguchi ▴ 40
23
votes
21
replies
13k
views
9 follow
fastest UMAP method
UMAP R
updated 22 months ago by ★ 30k • written 5.9 years ago by ▴ 40
1
vote
5
replies
1.6k
views
Isaac aligner V4 genome aligner questions
genome aligner BAM
22 months ago by DJBill ▴ 20
1
vote
0
replies
641
views
Blog: How to use random forest for clustering
computational-biology random-forest
updated 22 months ago by 45k • written 22 months ago by ★ 4.7k
1
vote
4
replies
1.1k
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 17 months ago by ▴ 40 • written 22 months ago by • 0
0
votes
0
replies
471
views
pathscan of MuSiC2 doesn't work
MuSiC pathscan dinglab
22 months ago by enho ▴ 60
0
votes
2
replies
865
views
Htseq Count
htseq htseq-count
22 months ago by Bjorn • 0
1
vote
6
replies
1.9k
views
frequency plot for peaks
chip-seq chipseeker
updated 22 months ago by ▴ 520 • written 22 months ago by ▴ 10
0
votes
0
replies
479
views
BWA mem -M option for gatk mutect
GATK mutect BWA NGS
updated 22 months ago by 154k • written 22 months ago by • 0
4
votes
2
replies
2.2k
views
GSEApy plot TypeError
gsea python DEG
updated 22 months ago by 45k • written 24 months ago by ▴ 70
1
vote
0
replies
865
views
Job: PhD position at K.G. Jebsen Center for Parkinson’s disease. Bergen, Norway.
omics phd
updated 22 months ago by 45k • written 22 months ago by ▴ 540
0
votes
0
replies
476
views
giraffe alignment for exome sequencing
vg alignment giraffe
updated 22 months ago by 45k • written 22 months ago by ▴ 30
0
votes
1
reply
744
views
annotatePeak error for some problem
ChIPseeker
updated 22 months ago by 45k • written 22 months ago by • 0
13
votes
10
replies
4.2k
views
Minimum requirements for a laptop to do rna seq analysis
chip-seq rna-seq ngs
updated 22 months ago by ★ 2.9k • written 22 months ago by ▴ 50
1
vote
3
replies
1.0k
views
Should unique gene names/transcript IDs be used for ribosomal gene copies in a GTF/GFF file?
GTF GFF
updated 22 months ago by ★ 3.1k • written 22 months ago by ▴ 950
5
votes
2
replies
5.6k
views
Biopython error: "ModuleNotFoundError: No module named 'Bio.SubsMat'"
biopython
updated 22 months ago by ▴ 20 • written 2.4 years ago by ▴ 220
0
votes
3
replies
998
views
Appropriate genome reference for converting TCGA VCF files to MAF
maf vcf vcf2maf TCGA
updated 22 months ago by ★ 1.3k • written 22 months ago by ▴ 70
1
vote
1
reply
771
views
RepeatModeler-2.0 BuildDatabase error
BuildDatabase RepeatModeler
updated 22 months ago by ★ 1.8k • written 22 months ago by • 0
0
votes
3
replies
2.5k
views
News: :: FINAL CALL :: A Practical Introduction to NGS Data Analysis (Nov 29 - Dec 1, 2023 in Munich, Germany) - only 2 seats left
DNA-Seq NGS RNA-Seq Workshop
22 months ago by David Langenberger 11k
121,961 results • Page 183 of 2440
Recent Votes
A: Which is the proper RNA-seq count table transformation to perform hierarchial cl
Answer: Differences between published differential gene expression results and own analy
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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Recent Replies
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
Honestly, those things shouldn't result in a considerable discrepancy. The largest difference will come from the post-processing & analysi…
Answer: Differences between published differential gene expression results and own analy by Ales ▴ 50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical by Mensur Dlakic ★ 30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy by yura.grabovska ▴ 830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria. by colindaven 8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2 by Olivia • 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
Comment: help with modkit on nanopore sequencing data. by andres.firrincieli 3.9k
On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
Comment: After doublet detection in 10x scRNA-Seq data, there is still evidence of double by yura.grabovska ▴ 830
Yes but the problem is that biological knowledge is never fully encompasing. While I can say that a cell expressing CD45 alongside astrocyt…
Comment: DNA copy number blacklist for excluding common unreliable regions by yura.grabovska ▴ 830
Human genome, ideally hg38
Comment: Is Newbler still available for download by anweshaash • 0
Hello, I am wondering if you got access to the software or not. I am looking to use Newbler for my research and I contacted Roche too but t…
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
> I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST. I assume you did the above to generate the transcriptome,…
Answer: With 10x Visum HD : How to map the barcode id to the barcode sequence ? by sacha ★ 2.5k
Got it https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-inclusion-list-formerly-barcode-whitelist
Comment: limmaFit error when comparing TCGA RNA-Seq data by vernonlim98 • 0
Thanks for the advice. Am still new to RNA seq and R programming in general, and will just do the analysis by myself.
Answer: The Biostar Handbook. A bioinformatics e-book for beginners. by Istvan Albert 103k
Update as of **August 2025**: The book now includes a new online course: [**FastTrack Bioinformatics 2025**][course] at no extra cost. Bio…
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