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can we subdivide a single .fa file having cds, cdna, protein and genomic sequence in to separate file having only one type of sequence?
bioconductor
updated 4.1 years ago by 45k • written 4.2 years ago by ▴ 40
3
votes
3
replies
1.2k
views
Ngs : how check if two samples come frome the same family?
exome family Genome
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 120
0
votes
2
replies
1.2k
views
program/ software to generate large synthetic benchmark gene/ protein interaction network
PPI interaction benchmark network R
4.2 years ago by cwwong13 ▴ 40
0
votes
0
replies
939
views
Job: Bioinformatics position at NIOO-KNAW (Wageningen, The Netherlands)
python snakemake Linux git Netherlands
4.2 years ago by m.dehollander ▴ 50
3
votes
1
reply
1.0k
views
identification of lncRNA
lncRNA mRNA RNA-seq
updated 4.2 years ago by ★ 2.6k • written 4.2 years ago by ▴ 30
6
votes
18
replies
6.7k
views
6 follow
How to generate a combined read count txt file with header as file name
bash linux awk R
updated 4.0 years ago by ▴ 10 • written 6.0 years ago by ▴ 470
2
votes
4
replies
2.2k
views
whole genome sequence for origami 2 (DE3) and rosetta 2 (DE3)
ecoli cells rosetta2 origami2 competent Novagen
updated 3.3 years ago by • 0 • written 4.2 years ago by ▴ 200
1
vote
2
replies
1.2k
views
Is geneontology.org down?
database geneontology
4.2 years ago by EagleEye 7.6k
3
votes
4
replies
1.6k
views
population stratification for candidate gene association study
stratification candidate population PCA gene
4.1 years ago by putty ▴ 40
9
votes
9
replies
5.1k
views
6 follow
Forum: Choose between AMD and INTEL Server CPU in 2021-2022
hardware server
updated 4.2 years ago by 27k • written 4.2 years ago by ▴ 140
0
votes
0
replies
1.2k
views
HiC matrix in .txt format to .h5
matrix HiC h5 txt
4.2 years ago by Oleczkaff • 0
2
votes
2
replies
1.1k
views
Genotype imputation - do SNP IDs of input files and reference panels matter?
genotype SNP reference VCF imputation
updated 4.2 years ago by 2.9k • written 4.2 years ago by ▴ 180
2
votes
1
reply
1.3k
views
Why am I getting microRNA genes from a 10X genomics dataset?
RNA-seq microRNA
4.2 years ago by Gene_MMP8 ▴ 240
1
vote
0
replies
1.2k
views
QIIME2 quality control
control dada2 quality qiime2
4.2 years ago by blur ▴ 280
0
votes
0
replies
1.6k
views
Job: Postdoc – Natural Language Processing / Text Mining
NLP PyTorch Text Mining Tensorflow
4.2 years ago by info ▴ 80
2
votes
4
replies
1.6k
views
How to create gene level data from a probe level data?
R sum mean gene microarray
4.2 years ago by mohammedtoufiq91 ▴ 270
3
votes
4
replies
1.6k
views
DENOVO ASSEMBLY
assembly NGS Assembly Denovo
updated 4.2 years ago by ★ 3.3k • written 4.2 years ago by ▴ 30
1
vote
4
replies
1.7k
views
SNP ID
SNP ID dbSNP_143
4.2 years ago by shamsurrahaman132 ▴ 10
1
vote
4
replies
6.6k
views
How to fix "ValueError: not enough values to unpack (expected 3, got 1)" when excuting batch analysis?
batch germline cnv
updated 4.2 years ago by • 0 • written 5.0 years ago by • 0
4
votes
4
replies
1.3k
views
What is the difference between Assignment and Prediction?
protein protein-structure protein-structure-prediction
updated 4.2 years ago by ★ 29k • written 4.2 years ago by ▴ 20
0
votes
5
replies
1.8k
views
CNVkit Feedback about panel or normales needed
CNVkit
4.2 years ago by mphoeppner • 0
2
votes
0
replies
682
views
panelcn.mops package to build up control.bam file
panelcn.mops samtools
4.2 years ago by jimmy0958073736 ▴ 40
1
vote
3
replies
1.2k
views
Blast results processing lines bigger than 60
blast unix commands awk result
4.2 years ago by hdtms ▴ 20
0
votes
14
replies
2.6k
views
error relate to R
TWAS SNP R
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 150
1
vote
0
replies
1.1k
views
DepthPerSampleHC and StrandBiasBySample HaplotypeCaller Warnings in GATK
Haplotypecaller
4.2 years ago by Jianing ▴ 10
2
votes
0
replies
625
views
scRNA-seq datasets for different cell lines
scRNAseq
4.2 years ago by Alexander ▴ 220
2
votes
9
replies
3.1k
views
Getting command line blastn results for the complementary strand
blast command-line blastn
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 70
2
votes
2
replies
1.2k
views
Differentially gene expression multispecies
Gene Expression Multiespecies RNAseq
4.1 years ago by tiagobellintani ▴ 40
3
votes
2
replies
1.3k
views
Differentially gene expression analysis using limma
Limma packages
updated 4.2 years ago by 3.3k • written 4.2 years ago by ▴ 20
2
votes
5
replies
2.5k
views
Weird characters in yeast reference gff3
SGD gff3 yeast gff
4.2 years ago by liorglic ★ 1.5k
7
votes
3
replies
1.8k
views
How to normalize and transform RNA-seq data of different samples for PCA?
TMM PCA RNA-seq edgeR
updated 4.2 years ago by 89k • written 4.2 years ago by ★ 1.1k
0
votes
2
replies
2.1k
views
Manhattan plot p-value
manhattan plot snp
4.2 years ago by shamsurrahaman132 ▴ 10
0
votes
0
replies
635
views
IGV add contig/chr to genome file within session
genome IGV bam alignment
4.2 years ago by noodle ▴ 650
0
votes
1
reply
1.1k
views
Which error bar to use to show gene expression from single-cell RNAseq data
expression rnaseq statistics gene single-cell
4.2 years ago by gundalav ▴ 380
0
votes
0
replies
1.6k
views
Generating comprehensive data for Promethease and Codegen.eu from WGS
WGS gVCF Promethease raw calling variant
4.2 years ago by Tim • 0
0
votes
0
replies
676
views
rsem-calculate-expression error
RNA-Seq rsem rsem-calculate-expression
4.2 years ago by Bhoomika • 0
3
votes
4
replies
1.4k
views
How to calculate the distribution of histone modifications on transcription factors
modifications histone
4.2 years ago by koyee_d ▴ 20
2
votes
2
replies
2.5k
views
How to convert genotypes "1, 2" to "0,1, 2"?
snp plink
updated 24 months ago by ▴ 10 • written 4.2 years ago by ▴ 50
0
votes
2
replies
891
views
Extracting coding region for multiple sequences.
Coding Region
4.2 years ago by QAZ ▴ 20
2
votes
8
replies
4.7k
views
Trying to run FIMO from Meme suite using command line
meme motif
updated 4.2 years ago by 11k • written 4.2 years ago by • 0
3
votes
3
replies
1.0k
views
How to identify and characterize novel genes?
Novel
updated 4.2 years ago by ▴ 590 • written 4.2 years ago by • 0
0
votes
0
replies
655
views
How was hierarchical clustering established for mRNA expression data?
clustering mRNA expression
4.2 years ago by ceruleanivy ▴ 50
0
votes
1
reply
1.1k
views
Help with processing GSE63060: Illumina data that does not have lumi requirements
lumi illumina Bioconductor R
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
1
vote
1
reply
1.1k
views
Minimum coverage for structural variant calling
variant structural coverage
updated 4.2 years ago by ★ 2.2k • written 4.2 years ago by ▴ 370
11
votes
10
replies
12k
views
7 follow
How To Calculate Genetic Heterogeneity From Genotype Data - How Useful Is This Measure?
genetics snp genotyping
updated 3.5 years ago by 45k • written 14.6 years ago by 16k
1
vote
3
replies
3.9k
views
Adding a chain ID (A or B etc) to my pdb file
pdb
updated 4.2 years ago by • 0 • written 4.6 years ago by • 0
0
votes
3
replies
3.8k
views
Problems running gatk - gatk: command not found
vcf bam gatk
updated 4.2 years ago by ★ 1.2k • written 4.2 years ago by ▴ 210
1
vote
0
replies
766
views
Job: Computational research positions, incl. postdoctoral scholars (recommender systems in genomics)
recommender Seattle visualization genomics
4.2 years ago by meuleman ▴ 10
0
votes
1
reply
1.2k
views
Exporting Genes/Molecules of interest from IPA Canonical Pathway
core export data analysis ipa
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
1
vote
3
replies
1.5k
views
TEMP ,Type checker found wrong number of fields while tokenizing data line.
bedtools TEMP transposabale elements
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
121,804 results • Page 617 of 2437
Recent Votes
Universal Human Reference RNA Sample
Universal Human Reference RNA Sample
Are these 10x samples too low quality for downstream analysis?
Are these 10x samples too low quality for downstream analysis?
C: gmap error: Length XXXX of quality score differs from length XXX of nucleotides
Answer: Question about substitution of KEGG
Answer: Universal Human Reference RNA Sample
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Recent Replies
Comment: Help with metagenomics viral by cfos4698 ★ 1.1k
It's possible/likely that your sequencing simply didn't recover any virus reads, despite RT-PCR detection. Often there is too much 'other s…
Answer: Split chromosome into smaller fragments to save memory when build xg and gcsa in by Jordan M Eizenga ▴ 740
I would say the answer is unfortunately no. It would be possible to make smaller individual XG indexes, but downstream subcommands in the V…
Comment: Question about substitution of KEGG by dxh0222 ▴ 10
Thanks for your recommendation! I think kofam_scan is suitable for me.
Comment: How to use CAFE from Orthofinder Results by san96 ▴ 190
Hi, are you referring to Orthogroups.GeneCount.tsv? Thank you.
Comment: Universal Human Reference RNA Sample by michael.j.apostolides ▴ 80
For example you can see it here, this is the first one in the table (SRR1215996): https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=ru…
Answer: Universal Human Reference RNA Sample by michael.j.apostolides ▴ 80
I believe here: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP025982 They are from the SEQC https://www-nature-com.proxy3.library.…
Answer: Question about substitution of KEGG by Mensur Dlakic ★ 29k
There is a tool that uses KEGG hidden Markov models and HMMer to scan individual proteins. It is not automated and may require some fiddlin…
Comment: Huge discrepancy between Pipseeker & DRAGEN for Pipseq data by 1769mkc ★ 1.3k
DRAGEN are you using dragen 4.4 release for your workflow?
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs by Jeremy Leipzig 23k
Your strategy sounds ok but we would need to see your modified file and the exact command you ran to know what happened.
Comment: Huge discrepancy between Pipseeker & DRAGEN for Pipseq data by Arindam ▴ 10
I think for mapping to the reference genome
Comment: Local Synteny Analysis with Uncharacterized Genes by Joe 22k
+1 for `clinker`, came here to make the same suggestion
Comment: Help with metagenomics viral by CECEL • 0
Hi, thanks for answer! I'm using Kraken2, but the classified reads, when put on BLAST, didn't returned nothing, even in Viruses_db...
Comment: How to obtain a refFlat file for the Rat by GenoMax 153k
You can't mix and match genomes and annotation as we discussed in the prior thread. Are you using the genome from UCSC, if you are using th…
Comment: Huge discrepancy between Pipseeker & DRAGEN for Pipseq data by 1769mkc ★ 1.3k
"DRAGEN uses a newer method employing hashtables" you mean the reference builder?
Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in by 李经纬 • 0
I use `vg construct --region chrom:start-end` to restrict graph to a chromosome region.
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