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121,907 results • Page 682 of 2439
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1
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5
replies
4.6k
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Miniconda InvalidArchiveError when downloading FastQC
conda fastqc
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 10
4
votes
2
replies
1.3k
views
Finding genes under positive selection in non-model species - Phylotranscriptomics approach ?
gene ortholog assembly rna-seq
updated 21 months ago by 45k • written 4.5 years ago by ▴ 1000
1
vote
4
replies
1.8k
views
problem with SNPs and Indels detectiong useng WGS data
WGS
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 280
0
votes
5
replies
2.0k
views
Using Statistical enrichment test for groups Principal Component Analysis
PCA
4.5 years ago by Gabriel ▴ 180
0
votes
4
replies
1.6k
views
How to create an heatmap of clusters obtained by degpatterns function?
R RNAseq degpatterns clusters DESeq2
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
620
views
How to predict gene promoters in Lactobacillus?
lactobacillus promoters
4.5 years ago by A_heath ▴ 170
1
vote
5
replies
2.0k
views
calculation synonymous and non-synonymous allele counts in a VCF file
VCF
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 30
1
vote
2
replies
2.9k
views
visualize phased vcf file
vcf phasing
updated 4.5 years ago by ▴ 600 • written 4.5 years ago by ▴ 290
1
vote
1
reply
2.1k
views
BLAT standalone version - why is it so slow?
BLAT
updated 4.5 years ago by 36k • written 4.5 years ago by • 0
0
votes
1
reply
2.4k
views
How to download individual-level genotype data from gnomAD or EXAC
data genotyping genome
updated 4.5 years ago by ▴ 270 • written 4.5 years ago by • 0
0
votes
0
replies
1.1k
views
miRDeep2 Support
miRNA mirDeep2
4.5 years ago by VineethVenumadhavan ▴ 50
2
votes
4
replies
6.4k
views
Visualizing VCF file on IGV
BCFTOOLS VCF IGV
updated 4.5 years ago by 153k • written 4.5 years ago by ★ 2.4k
6
votes
4
replies
4.4k
views
RSEM gene-level estimates to DESeq2
RNA-seq DESeq2 RSEM DGEA
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
2
votes
7
replies
5.2k
views
extract unmapped reads from the paired end samples using hisat2
pairedends hisat2 unmappedreads snakemake
4.5 years ago by winmoon6 • 0
0
votes
0
replies
639
views
How important is aligning BAM files to the appropriate design file?
gatk sequencing genomics wes bam
4.5 years ago by jon.klonowski ▴ 210
1
vote
8
replies
4.7k
views
Conserved markers between clusters (not between stim/exp etc)
Seurat Conserved Markers R
updated 4.5 years ago by • 0 • written 5.1 years ago by • 0
0
votes
6
replies
4.1k
views
Best compression for single cell RNA-seq object
seurat rna-seq scanpy single-cell scRNA-seq
updated 4.1 years ago by • 0 • written 4.5 years ago by ▴ 200
1
vote
2
replies
1.3k
views
Can we add additional columns to ped and map files in PLINK?
PLINK
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
2
votes
1
reply
2.8k
views
clusterProfiler GSEA for upregulated and downregulated gene sets: conflicting results
GSEA clusterProfiler DESeq2
updated 4.5 years ago by ▴ 60 • written 5.8 years ago by ▴ 30
11
votes
5
replies
3.7k
views
NovaSeq Duplicates
duplicationrate ChIP-seq
updated 3.2 years ago by 15k • written 4.5 years ago by ▴ 20
1
vote
4
replies
2.8k
views
How can I download the PCAWG (ICGC/TCGA) raw counts data?
ICGC RNA-Seq PCAWG
4.5 years ago by Sonia • 0
0
votes
1
reply
921
views
How do I determine antibiotic resistant gene from a metagenome
metagenomics genomics antibioticresistantgene
updated 4.5 years ago by ▴ 590 • written 4.5 years ago by ▴ 10
0
votes
1
reply
939
views
Converting REVIGO treemap csv to CirGO format
cirgo revigo
updated 4.5 years ago by 9.0k • written 4.5 years ago by ▴ 10
1
vote
2
replies
1.2k
views
makeblastdb performance benchmark
makeblastdb performance runtime memory blast
4.4 years ago by drquestion ▴ 20
6
votes
3
replies
1.7k
views
Running blastn to get best hits match using (-max_target_seqs 1 -max_hsps 1 ) ?
blast alignment
4.5 years ago by sunnykevin97 ▴ 1000
4
votes
3
replies
2.0k
views
Exporting the list of top loading genes from a particular principal component
PCAtools
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 80
1
vote
2
replies
1.9k
views
identifying strain using pangolin and nextclade
Covid19 pangolin nextstrain strain nextclade
4.5 years ago by eli_bayat ▴ 100
1
vote
0
replies
858
views
News: SBGNview: Data Analysis, Integration and Visualization of All Pathways
SMPDB PANTHER Reactome SBGNview Pathview
4.5 years ago by bigmawen ▴ 440
1
vote
4
replies
2.6k
views
HaplotypeCallerSpark
Variant gatk haplotypecaller
updated 3.5 years ago by • 0 • written 4.5 years ago by ▴ 120
2
votes
5
replies
3.0k
views
What is the most accurate short (ish) read aligner?
aligner sequencing bwa minimap2
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 120
0
votes
1
reply
986
views
MSI cslculation
bed sequencing annotation
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by • 0
0
votes
0
replies
952
views
How to covert VCF-like to ICGC-like vcf Format
conversion annotation
4.5 years ago by Alewa ▴ 190
6
votes
5
replies
3.5k
views
Comparison of samples to find the best parameters for RNA-seq
NGS rna fastq R sequencing
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 30
0
votes
1
reply
764
views
Problem featurecounts 0 assigned with canfam4, only less than 20% with canfam3 dog genome
rna-seq
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
8
votes
14
replies
3.8k
views
6 follow
Another infer_experiment.py interpretation question
RNA-Seq sequencing
updated 2.9 years ago by 153k • written 4.7 years ago by ▴ 20
0
votes
2
replies
1.1k
views
IF statement (in linux script) to merge Fastq files with similar (but not the same) names
unix script ifstatement linux fastq
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 40
2
votes
3
replies
1.9k
views
Add Strand tag to hisat2 alignments
rna hisat2
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 400
4
votes
4
replies
8.0k
views
Transcriptome assembly -- fastp vs Trimmomatic
trimming transcriptome
updated 13 months ago by ▴ 40 • written 4.5 years ago by ▴ 290
0
votes
1
reply
3.2k
views
How are SNP distance matrices made?
matrix SNP distance CFSAN pipeline
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 30
1
vote
2
replies
3.8k
views
Snakemake how to use glob_wilcards properly
glob wildcards snakemake python
4.5 years ago by Peter Chung ▴ 210
0
votes
3
replies
1.7k
views
RSEM Calculate Expression Error
rsem frequency coding RSEM sequencing
updated 4.3 years ago by ▴ 70 • written 4.5 years ago by • 0
1
vote
2
replies
1.5k
views
Why I get three file by makeblastdb?
blast
4.5 years ago by 153348734 • 0
10
votes
3
replies
3.8k
views
Blast hits output to fasta format ?
alignment assembly blast
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 1000
1
vote
5
replies
1.8k
views
DeSeq2 analysis - very low variability among replicates
edgeR deseq2 rnaseq
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 70
0
votes
0
replies
681
views
Charmm force field for octanoic acid
Charmm Gromacs Stimulation
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
1
vote
0
replies
608
views
Does GATK4 provide better quality of SNP/Indels calls over GATK3.8?
sequencing
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 10
0
votes
4
replies
5.0k
views
featureCount not processing reads
featureCounts RNA-Seq Rsubread
updated 4.0 years ago by 45k • written 10.8 years ago by ▴ 100
0
votes
1
reply
1.3k
views
How to create a dummy GFF file from fasta?
fasta coverage bed gff
4.5 years ago by O.rka ▴ 750
2
votes
2
replies
2.1k
views
is quality evaluation of transcriptome assembly still required if my workflow is (good quality reads (fastp) -> bowtie2 alignment to reference genome…
RNA-seq transcriptome
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 180
1
vote
2
replies
2.8k
views
single cell sequencing data doublets removal tools selection
sequencing
updated 4.5 years ago by ★ 2.1k • written 6.3 years ago by ▴ 350
121,907 results • Page 682 of 2439
Recent Votes
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
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