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210 results • Page
2 of 5
Sort: Views
Rank
Views
Votes
Replies
4
votes
7
replies
724
views
How to subtract a number from protein IDs?
blast
updated 5 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
8
votes
10
replies
720
views
Inflated GWAS test statistic after merging multiple batches of genotype dataset imputed differently
genotype
imputation
gwas
updated 6 days ago by
LauferVA
3.7k • written 7 days ago by
Amy
▴ 20
1
vote
2
replies
719
views
Job:
Scientist Position, Data Science AI/ML for Biology (JRD DS)
Data-Science
JNJ
Janssen
updated 1 day ago by
Ram
40k • written 13 months ago by
Shicheng Guo
★ 9.3k
0
votes
4
replies
714
views
Is there a way to get a list of all homogygous sites for each sample with plink (regardless if they are in a run)
plink
updated 2 days ago by
chrchang523
10k • written 17 days ago by
curious
▴ 730
7
votes
3
replies
713
views
blastn with short sequences gives no results in the corresponding genome
primers
blastn
updated 5 days ago by
Ram
40k • written 2.7 years ago by
A_heath
▴ 140
0
votes
5
replies
711
views
Can vg take MUMmer output as input?
vg
updated 14 hours ago by
Ram
40k • written 2.8 years ago by
ac2278
▴ 20
1
vote
3
replies
673
views
How to determine plasmid or chromosomal origin?
plasmid
chromosomal-origin
updated 5 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
1
vote
5
replies
667
views
Mugsy percentage of identity
Mugsy
Genome-alignment
updated 5 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
0
votes
13
replies
663
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn
Trinity
Transcriptome
RNA-seq-analysis
De-novo-transcriptome-assembly
4 days ago by
langziv
▴ 50
13
votes
10
replies
623
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 1 day ago by
ATpoint
76k • written 4 days ago by
MVJ
▴ 10
2
votes
3
replies
600
views
How to change standard genetic code in Artemis?
Mycosplasma
Artemis
updated 5 days ago by
Ram
40k • written 2.8 years ago by
A_heath
▴ 140
0
votes
0
replies
595
views
Contig extension using PRICE
price
updated 5 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
10
votes
8
replies
576
views
Adding a control sample to bulk RNA-seq
RNA-seq
5 days ago by
Chris
▴ 180
3
votes
7
replies
564
views
Identifying transcription factors for a list of genes
transcription-factor
updated 1 day ago by
Ram
40k • written 29 days ago by
lbombini
• 0
4
votes
8
replies
563
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
1 day ago by
Edoardo
• 0
0
votes
13
replies
560
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
3 days ago by
Y
• 0
5
votes
4
replies
560
views
How to correct a wrong protein extraction from FASTA file?
fasta
bash
updated 5 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
0
votes
2
replies
557
views
module and trait correlation for WGCNA
treatment
WGCNA
relation
microarray
module-treatment
updated 6 days ago by
AS-git
• 0 • written 6 months ago by
Shriyansh
• 0
6
votes
8
replies
517
views
Find potential important genes from bulk-RNA seq experiment
RNA-seq
4 days ago by
Chris
▴ 180
3
votes
10
replies
501
views
STAR index not working
STAR
RNA-Seq
5 days ago by
camillab.
▴ 130
0
votes
7
replies
486
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
2 days ago by
cwwong13
▴ 20
5
votes
7
replies
477
views
Elusive syntax error in Snakefile
snakemake
updated 6 days ago by
Ram
40k • written 7 days ago by
Giuseppe Giovanni
▴ 30
3
votes
2
replies
469
views
Conflict between MAFFT and new PRANK installation
multiple-sequence-alignment
bash
prank
mafft
phylogenetics
updated 6 days ago by
Ram
40k • written 19 months ago by
noramarie
• 0
3
votes
6
replies
468
views
summarize consecutive columns over a data frame
tidyverse
r
offtopic
updated 4 days ago by
Ram
40k • written 15 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
8
replies
462
views
Read block operation failed with BAM file
bgzip
samtools
bam
pysam
htslib
updated 19 hours ago by
John Marshall
3.0k • written 8 days ago by
Alex Reynolds
35k
1
vote
2
replies
456
views
Virtual box
virtual-machine
offtopic
updated 4 days ago by
Ram
40k • written 7 months ago by
georgeof35
• 0
2
votes
5
replies
453
views
Uniprot Database for download
proteomics
Uniprot
updated 5 days ago by
Elisabeth Gasteiger
★ 2.3k • written 4 weeks ago by
SHN
▴ 40
0
votes
2
replies
452
views
Average Coverage after Assembly (Spades)
coverage
average
assembly
updated 23 hours ago by
taniapsduarte
• 0 • written 13 months ago by
davidmaimoun
▴ 50
0
votes
5
replies
433
views
genome data downloads for various strains
gisaid
hass-marr
updated 1 day ago by
Ram
40k • written 5 days ago by
iftikharmaryam123
• 0
4
votes
2
replies
430
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 6 days ago by
yhdist
▴ 70 • written 9 days ago by
Cookin
▴ 10
0
votes
4
replies
422
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 3 days ago by
Jeremy Leipzig
21k • written 4 days ago by
Can Abdullah
• 0
5
votes
7
replies
417
views
Salmon index not progressing
salmon
updated 4 days ago by
Michael
53k • written 5 days ago by
camillab.
▴ 130
4
votes
4
replies
416
views
DESeq2 analysis using two featureCounts generated from different studies
RNA-seq
DESeq2
5 days ago by
abedkurdi10
▴ 190
2
votes
9
replies
414
views
Calculation of TMB on gene level
genomics
updated 17 hours ago by
svp
▴ 590 • written 1 day ago by
smrutimayipanda
▴ 20
3
votes
10
replies
395
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 10 hours ago by
ATpoint
76k • written 1 day ago by
arriyaz.nstu
▴ 30
3
votes
4
replies
388
views
Chromosome bias on RNA-Seq differential gene expression analysis
chromosome-bias
RNA-seq
4 days ago by
blz
▴ 30
0
votes
1
reply
381
views
Close genome comparison
Mauve
Mugsy
genome-comparison
GSAlign
updated 5 days ago by
Ram
40k • written 19 months ago by
A_heath
▴ 140
1
vote
2
replies
376
views
How to display all top markers in the heatmap by DoHeatmap (Seurat) when there are duplicates of top marker genes for several cell clusters
DoHeatmap
Seurat
6 days ago by
alwayshope
▴ 30
1
vote
3
replies
373
views
I have performed Trimmomatic run for adapter removal. QC report shows drop in the reads and presence of overrepresented sequences. Seeking help!
NGS
bioinformatics
illumina
WGS
updated 1 day ago by
swbarnes2
13k • written 1 day ago by
Vijith
▴ 30
3
votes
2
replies
365
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
2 days ago by
Thomas
▴ 20
0
votes
0
replies
363
views
Recommended workflow for identifying the genomic location and copy-number of an insert with a known sequence from WGS Nanopore fastq files
Nanopore
WGS
Long-Read
updated 5 days ago by
Ram
40k • written 6 days ago by
dk0319
▴ 70
0
votes
0
replies
361
views
Distinction of two very close bacterial strains
mutations
bacteria
updated 5 days ago by
Ram
40k • written 2.3 years ago by
A_heath
▴ 140
0
votes
5
replies
356
views
manhattan plot with vcf information
R
manhattan
vcf
updated 5 days ago by
dthorbur
▴ 550 • written 7 days ago by
sooni
▴ 10
3
votes
3
replies
355
views
Forum:
Importance of Data Structures for Bioinformatics?
data-structures
updated 5 days ago by
Ram
40k • written 6 days ago by
S
• 0
1
vote
3
replies
353
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 4 days ago by
Zhenyu Zhang
▴ 980 • written 6 days ago by
Mo
• 0
1
vote
5
replies
352
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 23 hours ago by
ATpoint
76k • written 5 days ago by
vk
▴ 40
7
votes
6
replies
348
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
updated 4 hours ago by
dsull
★ 4.7k • written 2 days ago by
Mehwish
• 0
4
votes
4
replies
346
views
Filtering VCF to divide with equal sizes
bcftools
vcf
updated 5 days ago by
Ram
40k • written 5 days ago by
avelarbio46
▴ 30
0
votes
8
replies
343
views
Violin plot (Monocle 3) - Troubleshooting
Monocle3
updated 8 hours ago by
Ram
40k • written 1 day ago by
seattlescientist_01
• 0
0
votes
0
replies
339
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
R
GEO
GEOmetadb
updated 4 days ago by
Pierre Lindenbaum
157k • written 4 days ago by
nonaddldy
▴ 10
210 results • Page
2 of 5
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Recent Replies
Comment: Which function is best for pathway analysis?
by
luffy
▴ 40
@chris Please look into @Hamid Ghaedi's well documented [post][1] on ORA and GSEA, Or [this][2] documentation. Hope this helps. [1]: ht…
Comment: Bacterial Pangenome Analysis
by
kirankumareripogu
▴ 10
Hi @liorglic, Thank you for your prompt response. I totally agree with you that different blastp cuttoffs provide different results and…
Answer: Fetch Fastq files directly for SRA data
by
Rob
6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe
by
YUYANG.OON
• 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
by
Chris
▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject
by
Qi
• 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis?
by
Yogi
▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions
by
Yogi
▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question
by
Istvan Albert
98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate
by
dsull
★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
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morovatunc
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Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
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53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate
by
Mehwish
• 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
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