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448 results • Page 2 of 9
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1
vote
4
replies
156
views
trying to look the version of the programs under miniconda3 directory
miniconda3 versions
updated 2 days ago by 68k • written 2 days ago by ▴ 90
1
vote
4
replies
3.9k
views
design primer for alternative splicing events
alternative-splicing primer-design RNA-Seq
updated 8 days ago by 37k • written 7.7 years ago by ▴ 450
0
votes
4
replies
1.9k
views
Dating Common Ancestor
ngs vcf
updated 23 days ago by 37k • written 8.9 years ago by ★ 2.6k
3
votes
4
replies
363
views
Changing Temporary File Location for Local BLASTP to nr Database
temporary blast file protein nr
10 days ago by katieostrouchov ▴ 20
3
votes
4
replies
285
views
Renaming fasta headers based on a list
fasta
updated 15 days ago by 37k • written 16 days ago by • 0
0
votes
4
replies
1.4k
views
Automate protein family analysis
protein-family
updated 19 days ago by 37k • written 7.7 years ago by ▴ 560
2
votes
4
replies
454
views
Unable to run RSEM because of error rsem-parse-alignments : No such file or directory
RNA-Seq Bowtie2 RSEM Boost
28 days ago by mohammedtoufiq91 ▴ 170
0
votes
4
replies
367
views
Does non-Mendelian equal to mutation?
mutation genetics Mendelian gene
16 days ago by solarchan7 • 0
0
votes
4
replies
209
views
vector memory exhausted (limit reached?)
escape seurat scGSEA Rstudio.
2 days ago by 50cf32b2 • 0
1
vote
4
replies
408
views
Custom made gff in geneious software - format conversion
format Geneious gff
11 days ago by L_bioinfo • 0
0
votes
4
replies
430
views
I want to merge gene sequences in fasta to create one genome from all cds region.
file manipulation fasta genome linux
17 days ago by iankeetkumar • 0
2
votes
4
replies
234
views
Ensembl ID to Gene Symbol Converter
ensembl Homo_sapiens BioMart biotools
updated 1 day ago by 125k • written 4 days ago by • 0
3
votes
4
replies
455
views
R package DESeq2 in R 3.5.1
packages installing error R
19 days ago by sehriban.buyukkilic • 0
0
votes
4
replies
10k
views
Convert .gbf file to .gbk or .gff
gbk gff gbf
updated 9 days ago by 37k • written 7.7 years ago by • 0
1
vote
4
replies
415
views
Stringtie issue. "Error: no valid ID found for GFF record"
Stringtie RNA-seq
updated 16 days ago by 125k • written 17 days ago by ▴ 40
1
vote
4
replies
3.4k
views
BWA MEM alignment output of splited fastq files differ from the original(unsplit) fastq file
next-gen alignment
updated 22 days ago by 37k • written 7.7 years ago by ▴ 70
0
votes
4
replies
413
views
Error in DNAmAge package in r
methylation DNAmAge
10 days ago by andrechristianes • 0
3
votes
4
replies
451
views
Snakemake not executing any tasks
python readqc Snakemake cutadapt
updated 21 days ago by ▴ 450 • written 23 days ago by ▴ 20
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq R
updated 25 days ago by 37k • written 7.7 years ago by ▴ 150
2
votes
4
replies
328
views
Differences between genomic position and genomic loci?
loci dna genome genetics gene
20 days ago by DS ▴ 20
2
votes
4
replies
326
views
Change sample ID in BAM file to cell barcode
bam samtools barcode scrna
6 days ago by martin.grasshoff • 0
5
votes
4
replies
3.4k
views
Black color reads in IGV: bwa-meth
IGV alignment bwa-meth
updated 24 days ago by 37k • written 7.7 years ago by ▴ 220
0
votes
4
replies
237
views
Running command in docker container results in directly shutting down the docker container
docker-container python ubuntu docker
2 days ago by stan.aanhane ▴ 30
1
vote
4
replies
1.4k
views
Uniprot to refseq missing entries
uniprot RNA-Seq refseq
updated 25 days ago by 37k • written 7.6 years ago by ▴ 40
0
votes
4
replies
3.8k
views
problem in installing zlibbioc library
R
updated 18 days ago by 37k • written 7.7 years ago by • 0
0
votes
4
replies
407
views
how to deal with missing genotype data (gt) to do a machine learning
missing_data
updated 19 days ago by ★ 2.9k • written 20 days ago by • 0
2
votes
4
replies
174
views
Calculate sequencing file size?
storage data sequencing plan management
updated 2 days ago by 125k • written 2 days ago by ★ 1.2k
0
votes
4
replies
2.0k
views
transforming data from Human Exon ST 1.0 to U133 Plus 2.0
expression-level
updated 29 days ago by 37k • written 7.6 years ago by • 0
4
votes
4
replies
699
views
Analysis of Nanopore cDNA sequencing data
alignment nanopore sequencing minimap2
2 days ago by Nico80 ▴ 60
0
votes
4
replies
449
views
how to perform gene ontology on genomic data?
GO
17 days ago by Neel ▴ 10
0
votes
4
replies
278
views
How to call somatic mutations from vcf files
cancer vcf bcf bam gene
updated 6 days ago by 152k • written 6 days ago by ▴ 20
0
votes
4
replies
2.6k
views
biomaRt: Extracting data for a particular isoform (R/bioconductor)
bioconductor utr biomart
updated 4 days ago by 37k • written 7.7 years ago by ▴ 210
2
votes
3
replies
486
views
Combining single-end and paired end reads
differential meta-analysis analysis expression
25 days ago by shri.au • 0
3
votes
3
replies
407
views
GO analysis: Different results EnrichGO vs ShinyGO
enrichGO GO RNA-seq shinyGO analysis
updated 18 days ago by 26k • written 19 days ago by ▴ 10
0
votes
3
replies
359
views
Trying to select a certain range of sequences in Geneious
Geneious
updated 20 days ago by 125k • written 24 days ago by • 0
0
votes
3
replies
212
views
How long does it take to apply for the academic license of Schrodinger Desmond?
Desmond Schrodinger
updated 9 days ago by 125k • written 10 days ago by • 0
1
vote
3
replies
348
views
PCA projection with --score plink2.sscore output: what are the ALLELE_CT & NAMED_ALLELE_DOSAGE_SUM showing?
pca-projection allele-dosage score plink2
updated 15 days ago by 9.9k • written 18 days ago by ▴ 20
0
votes
3
replies
2.6k
views
ReadVCF not reading samples
readVcf VariantAnnotation R
updated 18 days ago by 37k • written 7.7 years ago by ▴ 370
0
votes
3
replies
2.3k
views
Need help converting VCF 4.1 file to 4.0
next-gen
updated 22 days ago by 37k • written 7.7 years ago by ▴ 30
2
votes
3
replies
270
views
SALMON Index build Process Killed!
salmon index mapping
3 days ago by Soumajit ▴ 30
0
votes
3
replies
211
views
best way to learn bash scripting
bash coding sequncing
updated 1 day ago by ▴ 740 • written 1 day ago by • 0
0
votes
3
replies
427
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata functional-annotation BRAKER MAKER
updated 19 days ago by 7.5k • written 24 days ago by ▴ 20
2
votes
3
replies
10k
views
converting maf to vcf
Exome maf2vcf
updated 5 days ago by 37k • written 7.7 years ago by • 0
0
votes
3
replies
342
views
How to interpret deletion the length of chromosome?
del
updated 13 days ago by 152k • written 13 days ago by ▴ 100
1
vote
3
replies
178
views
Retrieve specific fasta sequences from a group of assemblies
CDS gene sequence
updated 1 day ago by 2.8k • written 1 day ago by ▴ 100
1
vote
3
replies
417
views
Combining TF PWMs
TF Jaspar motif PWM
19 days ago by rbronste ▴ 410
3
votes
3
replies
2.6k
views
Breast cancer TCGA data - DGE analysis
RNA-Seq Voom Raw_Count TCGA
updated 8 days ago by 37k • written 7.7 years ago by ▴ 460
0
votes
3
replies
392
views
What can I do with pan-cancer RNA-seq data that only has FPKM value?
normalization RNA-seq
updated 24 days ago by 68k • written 25 days ago by ▴ 10
1
vote
3
replies
210
views
difference between target sequencing technologies
capture sequencing hybrid wes
updated 1 day ago by 125k • written 1 day ago by ▴ 10
0
votes
3
replies
226
views
script for local blast to mapped primer to the genome
blast
updated 8 days ago by 20k • written 9 days ago by • 0
448 results • Page 2 of 9
Recent Votes
A: Using ColSums vs sizeFactors in read count normalization
Comment: a problem with getBM
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
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Recent Replies
Answer: how to do a reliable single cell sequencing analysis? by ATpoint 68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM by sanaz • 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v by fuellen ▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM by Mike Smith ★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)? by Fabio Marroni ★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism by Rob ▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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