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121,924 results • Page 78 of 2439
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2
votes
2
replies
1.0k
views
Only two fastqs for 10X scATAC-seq data deposited on GEO database.
scATAC-seq cellranger single-cell 10X
13 months ago by 1048686151 • 0
4
votes
3
replies
1.6k
views
IGV and display of amino acid translations
IGV amino-acids
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
0
replies
331
views
Using Arriba on single cell data set (scRNA-seq)
scrna-seq
13 months ago by sogand • 0
0
votes
2
replies
914
views
Obtaining clinical data from the TCGA data portal
Cancer hg38 TCGA
13 months ago by elisheva ▴ 120
0
votes
0
replies
359
views
Encoding protein sequences based on catalytic residues
of functional proteins annotation
updated 13 months ago by 153k • written 13 months ago by • 0
5
votes
6
replies
1.5k
views
Download files from Experiment Acession
BioProject NCBI SRA
13 months ago by Manuel Sokolov Ravasqueira ▴ 110
0
votes
0
replies
493
views
Generate the snpfile.txt (for BLUPF90 input) in 0125 format from plink flat file (.map and .ped)?
Genotype BLUPF90 PLINK
updated 13 months ago by 153k • written 13 months ago by ▴ 10
0
votes
6
replies
1.8k
views
Associate Roary output with locus_tag from specific genome
bacteria locus_tags genomics
updated 13 months ago by 22k • written 14 months ago by • 0
0
votes
5
replies
1.4k
views
Segmentation fault PLINK 1.90b
PLINK
updated 13 months ago by 11k • written 13 months ago by ▴ 30
1
vote
6
replies
2.6k
views
ROSE called super-enhancers overlapping with promoters
super-enhancers ROSE ChIP-seq
updated 13 months ago by ★ 19k • written 20 months ago by ▴ 10
0
votes
0
replies
872
views
Job: Bioinformatics Analyst - Laboratory Medicine and Pathology
job
13 months ago by toddknutson ▴ 60
2
votes
2
replies
875
views
Hard filtering to reduce false positive variants due to poly track sequences
GATK
updated 13 months ago by 153k • written 13 months ago by ▴ 110
0
votes
1
reply
844
views
A USER ERROR has occurred: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be us…
GATK VCF QD VariantRecalibrator
updated 13 months ago by ▴ 540 • written 13 months ago by • 0
0
votes
1
reply
1.6k
views
Treemix is taking too long running
treemix cutadapt ubuntu
updated 13 months ago by 56k • written 3.1 years ago by ▴ 40
2
votes
4
replies
1.2k
views
can someone please explain the DAPARS output?
RNA-seq APA DaPars2
13 months ago by PK ▴ 130
3
votes
7
replies
1.7k
views
How to create a tax_id_map file for getting scientific names in BLASTN output
BLAST NCBI
13 months ago by Maria • 0
0
votes
0
replies
329
views
What to do with ALDEx2 associations where p < 0.05, but the 95% confidence intervals bridge zero
Metagenomics ALDEx2 Differential-abundance
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
2
replies
676
views
low ribosomal protein in scrnaseq data
ribosomal-proteins scRNA-seq
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
1
reply
588
views
Redundant Database for BLAST search
database taxonomy phylogeny BLAST
updated 13 months ago by 153k • written 13 months ago by • 0
1
vote
1
reply
672
views
Should mutations in repetitive base positions be considered real
cancer DNA
updated 13 months ago by 22k • written 13 months ago by ▴ 10
0
votes
1
reply
896
views
Extracting Enhancer Regions from ENCODE Annotation Files
ENCODE enhancer
updated 13 months ago by • 0 • written 17 months ago by • 0
0
votes
3
replies
1.0k
views
VG - Verifying presence or absence of variants in Pangenome Graph
mutation variant pangenome vcf vg
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
0
votes
0
replies
1.1k
views
Using get_normalized_expression (scVI) vs. Log-Normalized Counts
scVI normalization RNA-seq single-cell UMAP
13 months ago by Nicolas • 0
0
votes
1
reply
476
views
Collapse technical replicates in DEGS
RNA-Seq DEGS Technical-replicates
updated 13 months ago by 45k • written 13 months ago by ▴ 10
1
vote
2
replies
764
views
Time-series statistics for a small amount of genes
rna-seq time-series
13 months ago by Aspire ▴ 390
0
votes
0
replies
447
views
News: Course - Introduction to R Shiny
R Web-Applications Shiny
13 months ago by Physalia-courses ★ 2.6k
1
vote
8
replies
1.9k
views
minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
minimap2
13 months ago by shinyjj ▴ 60
0
votes
1
reply
522
views
Isoforms and Transcriptome assembly with direct RNA Nanopore reads
isoforms assembly transcriptome sequencing nanopore
updated 13 months ago by 153k • written 13 months ago by • 0
6
votes
11
replies
5.7k
views
Randomly select a number of variants and samples from a multi-sample VCF file (pVCF)
vcf pvcf
updated 13 months ago by 56k • written 2.7 years ago by ▴ 330
3
votes
7
replies
2.0k
views
Need to split a cram file into smaller pieces - how to extract and save cram format to a new file?
samtools CRAM
updated 6 months ago by ▴ 10 • written 13 months ago by ★ 2.4k
1
vote
3
replies
841
views
Hybrid assembly with Unicycler and multiple files of input
unicycler assembly
updated 13 months ago by ★ 1.8k • written 13 months ago by ▴ 70
1
vote
3
replies
937
views
What should I use correlate/compare microbiome compositional data to other data types
R python microbiome compositional-biology
updated 13 months ago by ★ 3.1k • written 13 months ago by ▴ 50
0
votes
0
replies
437
views
How to Accurately Determine Unique Mapped Reads from HISAT2 Output summary file
mapped unique analysis Hisat2 RNA-seq
updated 13 months ago by 153k • written 13 months ago by ▴ 20
0
votes
0
replies
354
views
News: Course: Advance your Python Skills for Life Sciences
python vPython Pythonlang
updated 13 months ago by 45k • written 13 months ago by ▴ 70
0
votes
0
replies
354
views
News: Course: Introduction to R
Rproject Rlang Rstats
updated 13 months ago by 45k • written 13 months ago by ▴ 70
1
vote
2
replies
924
views
R package to visualize multiple aligned chromatograms
R plot chromatogram Sanger
13 months ago by DaniCee ▴ 20
0
votes
3
replies
907
views
issue with terms label in Go dotplots
R clusterProfiler GO-terms
13 months ago by G.S ▴ 60
0
votes
0
replies
375
views
BCftools call when using -v -V indels vs using -V indels only
BCftools plink
13 months ago by Jimmy M • 0
4
votes
5
replies
1.2k
views
How to make the length of the CDS of my bed file divisible by 3?
annotation CDS TOGA bed
updated 13 months ago by 56k • written 13 months ago by • 0
0
votes
0
replies
500
views
News: Course: Introduction to the Analysis of Longitudinal Data in Biology Using R
Longitudinal-Data R Epidemiology Forecasting Gene-Expression
updated 13 months ago by 45k • written 13 months ago by ★ 2.6k
5
votes
8
replies
1.8k
views
p-value/adjusted p-vlaue cutoff
adjusted-pvalue p-value DESeq2 fgsea
updated 13 months ago by 27k • written 13 months ago by • 0
0
votes
1
reply
771
views
bamCoverage - how BPM normalization was done?
bamcoverage chip-seq deeptools
13 months ago by Pei ▴ 240
0
votes
0
replies
384
views
Help needed to troubleshoot : conversion error with open babel on cmd
open-babel
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
0
replies
398
views
No MAF filtering for GWAS
GWAS
updated 13 months ago by 45k • written 13 months ago by ▴ 20
3
votes
4
replies
1.1k
views
DNA SPRITE Expirment Benchmark
SPRITE Genome
updated 13 months ago by 45k • written 13 months ago by • 0
1
vote
5
replies
1.4k
views
Centrifuge Index creation issue
metagenomics centrifuge
13 months ago by skbrimer ▴ 740
8
votes
6
replies
1.5k
views
Non-existent transcript as a result from Salmon
RNAseq salmon
13 months ago by Vojtěch ▴ 10
2
votes
1
reply
717
views
How to calculate differentially spliced genes in single cell?
scrna velocyto splicing scvelo
updated 13 months ago by 89k • written 13 months ago by ▴ 10
2
votes
2
replies
726
views
Basic coding-Stuck with Java script while working with KNIME
java
13 months ago by Sanjukta • 0
2
votes
2
replies
930
views
How can we determine or find the insertion time of Numts?
pacBio Bioinformatician mtDNA NUMTS
13 months ago by hashim.rana11 ▴ 40
121,924 results • Page 78 of 2439
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C: Counting Number Of Bases In A Fastq File
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Recent Replies
Comment: Orthofinder Not Mapping to Any Orthogroups by saamhasan55 ▴ 10
I checked the file and it's definitely proteins. I had previously run BUSCO on protein mode on the same file and got >90% completeness. I r…
Comment: Orthofinder Not Mapping to Any Orthogroups by saamhasan55 ▴ 10
I ran BUSCO on the predicted proteome in protein mode and got >91% completeness. I also removed multiple isoforms from the same gene.
Comment: Help with Model by Stele • 0
Hey, thanks for the reply! I think I didn't make the question very understandable. I do know how to code for this, the wall I have hit is *…
Comment: Orthofinder Not Mapping to Any Orthogroups by Mensur Dlakic ★ 30k
Not enough detail to make a definitive recommendation. Since this should not happen, an educated guess is that you are doing something wron…
Comment: Orthofinder Not Mapping to Any Orthogroups by Michael 56k
A reason may be that your gene prediction is off. Did you run BUSCO on your predicted proteome? If the gene prediction is ok, then you shou…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
> Can you comment on these, If they look good ? More importantly how do these assemblies compare (contiguous/number of chromosomes/size) t…
Comment: TOPMed Imputation - More than 10000 allele switches by Qianshu • 0
Hi, I have the same error with you, have you sorted it out yet? If you have, could you please share some? Thank you!
Comment: Genome Assembly QC from BAM files by colindaven 7.9k
yes they look excellent
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
hello @colindaven I ran the INSPECTOR tool you mentioned on the genome assemblies. Below are stats for one of my sample (othere were simi…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by Christopher ▴ 10
You are right. I initially decided to keep Cutadapt because I feel more confident using it for primer removal, and it is the tool most comm…
Answer: Help with Model by i.sudbery 22k
I'm not quite sure what you are asking. Stochastic reaction networks like this can be coded using the Gillespie algorithm. Genes being …
Comment: miRNA low mapping ratings by Ant ▴ 50
No, these are from the total reads, but when considering only the reads with adapter, I checked MultiQC again and it’s around 10–20% when a…
Comment: miRNA low mapping ratings by GenoMax 153k
> the total number of reads is very low (around 1–10% of the total reads) Are these the reads that actually have the QIAseq 3'-miRNA adapt…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by GenoMax 153k
> cutadapt > bbduk > bowtie2 > qiime2 > dada2 > kraken2 > krona Curious as to why you have `cutadapt` and `bbduk`. `bbduk` should be able…
Comment: miRNA low mapping ratings by i.sudbery 22k
As GenoMax said, the most likely thing to me here is that there is nothing cloned into the library. I can't think of any bioinformatic reas…
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