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122,034 results • Page 579 of 2441
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0
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2
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1.3k
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How to download fasta sequence of my interest from NCBI?
NCBI FASTA
updated 3.3 years ago by 45k • written 4.1 years ago by ▴ 170
1
vote
6
replies
2.0k
views
scRNASeq analysis Transcript abundance and gene abundance
abundance quantification scrnaseq transcript
4.1 years ago by SG ▴ 20
1
vote
4
replies
3.0k
views
Deseq2 - how to save zero counts on normalization step
deseq2 normalization
4.1 years ago by Sandhiya ▴ 20
1
vote
1
reply
1.4k
views
Job: Bioinformatics Scientist
scientist pharmaceuticals
updated 2.9 years ago by 45k • written 4.1 years ago by ▴ 10
1
vote
3
replies
3.5k
views
Samtools - [main_samview] fail to read the header
bam samtools
updated 4.1 years ago by 45k • written 4.1 years ago by ▴ 110
1
vote
1
reply
1.0k
views
Refseq annotation for processed/unprocessed Pseudogenes
refseq pseudogene annotation genomics
updated 4.1 years ago by 154k • written 4.1 years ago by ▴ 60
9
votes
2
replies
6.1k
views
Clustering resolution for scRNA-seq
clustering single-cell
updated 4.1 years ago by ★ 1.7k • written 4.1 years ago by ▴ 10
0
votes
1
reply
684
views
promoter and insulator data download
promoter insulator data
updated 5 months ago by ▴ 100 • written 4.1 years ago by • 0
0
votes
0
replies
675
views
Single cell rna seq (scRNA Seq) analysis - TRANSCRIPT /GENE ABUNDANCE OR QUANTIFICATION
scRNA quantification gene transcript
4.1 years ago by SG ▴ 20
0
votes
4
replies
3.4k
views
Kraken2 output visualisation with Krona Viruses not shown
metagenomics kraken2 krona virus
4.1 years ago by maja.nackenhorst • 0
2
votes
3
replies
3.9k
views
selscan not outputting ihs
selscan haplotypes vcf
updated 4.1 years ago by ▴ 10 • written 6.5 years ago by ▴ 170
0
votes
0
replies
771
views
Rvtests SKAT-O output
rvtests sequencing SNP
4.1 years ago by @anna • 0
2
votes
0
replies
1.6k
views
Remove related samples using plink
plink ibd pihat plink2
4.1 years ago by sumudu_rangika ▴ 50
4
votes
3
replies
1.2k
views
Remove text and add a string in odd rows in a fasta file using awk
awk
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 30
5
votes
2
replies
1.3k
views
FFPE and fresh-frozen samples in different RNA seq batches?
batch RNA-seq fresh-frozen FFPE
4.1 years ago by Axel ▴ 10
1
vote
1
reply
903
views
Editing header of a fasta file
headers fasta
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 10
0
votes
2
replies
1.6k
views
How do I determine p-value and fold change for TMM normalized data?
TMM P-value normalization
updated 4.1 years ago by 89k • written 4.1 years ago by • 0
0
votes
3
replies
1.7k
views
Dragen-gatk pipeline information ?
germline gatk dragen wgs
updated 4.1 years ago by ★ 3.0k • written 4.1 years ago by ▴ 120
0
votes
0
replies
959
views
Error in merged bam files
picard GATK NGS
4.1 years ago by priya.bmg ▴ 70
0
votes
0
replies
556
views
What are the steps of an full lengh RNA seq annotation method?
genome-annotation
4.1 years ago by ilante ▴ 30
1
vote
11
replies
3.5k
views
desEQ2 eRROR
featurecount NA DESeq2 values
4.1 years ago by Nai ▴ 50
0
votes
0
replies
885
views
Herald: The Biostar Herald for Tuesday, September 14, 2021
herald
4.1 years ago by Biostar 3.6k
0
votes
0
replies
597
views
How to create phylogenic tree from NCBI taxon ID-s
tree phylogenic R
4.1 years ago by Roland • 0
0
votes
2
replies
1.2k
views
What is the difference between filtering cells before creating Seurat object and after that?
Seurat filter cells
4.1 years ago by re_raz ▴ 90
0
votes
2
replies
1.0k
views
Genome mapping and annotation
annotation genome
4.1 years ago by claudia • 0
0
votes
0
replies
890
views
Job: Post-doctoral position in bioinformatics for the analysis of enzyme families from metagenomic data, Evry, France
enzyme functional-annotation metagenomic postdoc
updated 2.7 years ago by 45k • written 4.1 years ago by • 0
0
votes
0
replies
649
views
Job: Post-doctoral position in bioinformatics for the analysis of enzyme families from metagenomic data, Evry, France
enzyme functional-annotation metagenomic postdoc
updated 2.7 years ago by 45k • written 4.1 years ago by • 0
5
votes
2
replies
1.7k
views
Kallisto Bootstrapping and deseq2
Deseq2
4.1 years ago by Mozart ▴ 330
2
votes
2
replies
1.0k
views
Batch correction for DE analysis
batch-correction mRNA RNA-seq DEGs MDSplot
updated 18 months ago by 45k • written 4.1 years ago by ▴ 10
4
votes
2
replies
1.8k
views
Genome indexing with hisat2 and samtools
samtools index Hisat2 RNA-seq genome
updated 4.1 years ago by 154k • written 4.1 years ago by ▴ 40
0
votes
0
replies
791
views
Primer3 issue with the Sequence_ID
primer3
4.1 years ago by aka ▴ 10
0
votes
0
replies
995
views
DESeq2 treated vs untreated and contrast vs no contrast
DESeq2 RNAseq
4.1 years ago by User000 ▴ 750
3
votes
4
replies
2.2k
views
Trinity after trimmomatic
Trinty Trimmomatic merge paired
4.1 years ago by Princy ▴ 60
1
vote
0
replies
669
views
How codeml detects positive selection
PAML CODEML
4.1 years ago by Amay ▴ 10
0
votes
0
replies
698
views
Reads preparation steps for amplicon metagenomics
PCR Metagenomics
4.1 years ago by Denis ▴ 320
0
votes
1
reply
1.0k
views
Mark duplicates the bam files sorted by coordinates
Spark duplicates Mark
updated 4.1 years ago by 4.2k • written 4.1 years ago by ▴ 70
1
vote
3
replies
1.4k
views
SIte Mutations in a 3D protein structure to locate the core of mutations
3D structure mutations protein
updated 4.1 years ago by ★ 30k • written 4.1 years ago by ▴ 80
1
vote
3
replies
1.6k
views
How to depict edges as an indicator of no. of frames in which two residue interact in Residue interaction network using Cytoscape?
RIP-MD RIN MD-simulation Cytoscape
updated 4.1 years ago by 27k • written 4.1 years ago by • 0
0
votes
0
replies
1.1k
views
'Can\'t connect to eutils.ncbi.nlm.nih.gov:443'
to Cant eutils.ncbi.nlm.nih.gov connect
4.1 years ago by Akbar • 0
1
vote
1
reply
866
views
What is the best way to generate snp list from reference genomes from NCBI?
snps
updated 2.7 years ago by 45k • written 4.1 years ago by ▴ 20
0
votes
5
replies
4.3k
views
low FRiP(Fraction of Reads in Peaks) score in ATAC-seq
ATAC-seq FRiP ATAC
updated 4.1 years ago by 89k • written 4.1 years ago by • 0
0
votes
0
replies
1.3k
views
SURVIVOR merge function usage
NGS genome genomics
updated 2.7 years ago by 45k • written 4.1 years ago by • 0
1
vote
2
replies
1.2k
views
custom reference panel
sample impute GWAS
4.1 years ago by raalsuwaidi ▴ 110
0
votes
1
reply
716
views
Extarction of hypervariable region
16S-RNA Bacteria Hypervariable-regions Pathogen
updated 2.7 years ago by 45k • written 4.1 years ago by • 0
1
vote
2
replies
971
views
How to download data for visualising and analysing in RINalyzer in Cytoscape.
RINalyzer RIN Cytoscape
4.1 years ago by Anjali • 0
0
votes
0
replies
761
views
Penalty for unexpressed genes
score Penalty
4.1 years ago by Sandhiya ▴ 20
11
votes
16
replies
7.8k
views
6 follow
NCBI NR protein db nr.gz FASTA inflate error?
DIAMOND NCBI alignment Megan6
updated 2.6 years ago by 45k • written 4.1 years ago by ▴ 30
0
votes
0
replies
639
views
How to perform principal component analysis (PCA) on topologically associating domain (TAD) data?
TAD PCA
4.1 years ago by ziyan • 0
3
votes
1
reply
1.1k
views
Forum: Which bioinformatics tool would you love to see running much faster?
Algorithm optimisation
updated 4.1 years ago by 36k • written 4.1 years ago by • 0
0
votes
1
reply
1.3k
views
The result of plink --freq is filled with NA
--freq vcf SNP NP PLINK
4.1 years ago by yoshifumimiya ▴ 50
122,034 results • Page 579 of 2441
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Answer: Choosing enrichment analysis tool
Answer: reference-guided assembly tools for short read data?
Answer: BWA-MEM with an array of files
Comment: BWA-MEM with an array of files
Answer: MOuse Testis Enhancer region
Dependent samples in DESeq2 - How to incorporate random factor?
Answer: Validating snRNA-seq cell type by correlating with other datasets
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Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq by LChart 5.1k
While Himar1 inserts in TA motifs, the library is generated following restriction enzyme treatment (Mmrl) and ligation. The Mmrl sequence i…
Comment: Is it possible to do standard GSEA in R? by mbramble • 0
See discussion at https://support.bioconductor.org/p/9142651/#9142680 concerning issues with preranked gsea.
Comment: BWA-MEM with an array of files by LChart 5.1k
For solution 1, because bwa streams the data, you can save some space by using a named pipe: ```bash mkfifo Sample_23/concat.R1.fq.gz find…
Comment: reference-guided assembly tools for short read data? by Hani • 0
Either de novo or reference based genome assembly using Illumina PE short reads
Comment: reference-guided assembly tools for short read data? by lieven.sterck 16k
which purpose specifically?
Comment: reference-guided assembly tools for short read data? by Hani • 0
In regards to your comment about synteny analysis, I suspected that would be the case. In regards to tools for these purposes, do you perso…
Comment: BWA-MEM with an array of files by lieven.sterck 16k
aha, but bwa mem only takes at best 1 pair of fastq files as input, not a whole list. So to achieve this efficiently do what https://www.b…
Answer: reference-guided assembly tools for short read data? by lieven.sterck 16k
Not silly at all and done before many times. So yes that is a valid approach. There are certainly a number of tools around that can do this…
Comment: BWA-MEM with an array of files by garcesj ▴ 50
None in particular (that's why I didn't indicate it). It just gives back the BWA-MEM help.
Answer: BWA-MEM with an array of files by Pierre Lindenbaum 166k
solution 1: merge each R1 and R2 files into one. Beware, the order of the fastq files must be the same find Sample_23 -type f -name …
Comment: BWA-MEM with an array of files by lieven.sterck 16k
what is the (error) message you get, if any?
Comment: MOuse Testis Enhancer region by Bioinformatics_16 • 0
![enter image description here][1] [1]: /media/images/0241beed-c410-47b0-b8e2-43534232
Answer: MOuse Testis Enhancer region by GenoMax 154k
It is not just you the site appears to be down right now: https://downforeveryoneorjustme.com/enhanceratlas.org?proto=http&www=1
Comment: Cells from normal sample were incorrectly classified as tumor cells using copyk by tujuchuanli ▴ 130
Since I'm running an automated pipeline to process multiple datasets, can I simply use the immune cells from CD45+ clusters in each dataset…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by PolenP ▴ 10
I used 16Gb RAM, with `--threads 8` but both with and without `--threads` function took the same time. It produced 58Gb each pair so far. I…
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