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122,004 results • Page 268 of 2441
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3
votes
7
replies
4.7k
views
HISAT2 relaxing parameters?
RNA-Seq HISAT2 alignment mapping mismatches
updated 2.5 years ago by ★ 2.1k • written 7.3 years ago by ▴ 10
1
vote
2
replies
893
views
color key heatmap
heatmap
2.5 years ago by kalyani ▴ 10
6
votes
2
replies
2.7k
views
R and R studio for Macbook
studio R
updated 2.5 years ago by ▴ 30 • written 2.5 years ago by • 0
0
votes
0
replies
657
views
Gene Expression Database for Mental Disorders
gene_expression_db
2.5 years ago by leenkhoury282 • 0
0
votes
0
replies
996
views
illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion
microarray illumina R probe-annotation
2.5 years ago by accibio ▴ 20
368
votes
82
replies
156k
views
35 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 18 months ago by ▴ 330 • written 12.7 years ago by ★ 4.5k
5
votes
3
replies
1.5k
views
How do i search a FASTA database by sequence in seqkit?
seqkit rRNA genomics 16s gene
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 10
3
votes
3
replies
2.9k
views
Read counting in RSEM and Salmon (alignment mode)
quantification RSEM RNA-seq Salmon
2.5 years ago by predeus ★ 2.1k
62
votes
14
replies
206k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 2.5 years ago by 12k • written 12.7 years ago by ▴ 930
4
votes
5
replies
8.1k
views
edgeR, Pseudobulk scRNA-seq
seurat scrna-seq edgeR
updated 2.5 years ago by ★ 8.3k • written 2.5 years ago by ▴ 30
2
votes
3
replies
1.6k
views
fitting a copy number profile to know CNV signatures
CNV copy number LOH CNA
updated 2.4 years ago by 4.8k • written 2.5 years ago by ★ 1.4k
0
votes
1
reply
796
views
Error in change Affymetrix transcript cluster id to Gene Symbol in microarray
microarray id cluster Affymetrix transcript
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 10
0
votes
0
replies
507
views
Hub Genes Verification
hub_genes
2.5 years ago by leenkhoury282 • 0
5
votes
4
replies
2.0k
views
BLASTN for very short sequence
blastn
2.5 years ago by yas ▴ 20
2
votes
3
replies
1.0k
views
why the metabolomics file does not merge?
R
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 20
3
votes
4
replies
1.3k
views
WGCNA problem
WGCNA
updated 2.5 years ago by 3.9k • written 2.5 years ago by • 0
1
vote
1
reply
2.0k
views
Installing pybedtools in Windows 10
pybedtools
updated 2.5 years ago by 22k • written 2.5 years ago by ▴ 140
0
votes
0
replies
873
views
In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
2.5 years ago by Neel ▴ 20
1
vote
3
replies
1.2k
views
RibORF perl script
rib-seq perl riborf
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 90
0
votes
0
replies
554
views
Plink2 haplotype results interpretation
plink2
2.5 years ago by alva • 0
1
vote
1
reply
1.0k
views
Positive and negative value fold value in ATAC seq using DiffBind
ATAC seq
updated 2.5 years ago by ★ 2.1k • written 2.5 years ago by ▴ 360
0
votes
2
replies
990
views
colour background on lables from EnhancedVolcano in R
Volcanoplot EnhancedVolcano R
2.5 years ago by Astrid • 0
8
votes
10
replies
3.3k
views
How to convert GTF output of TSEBRA to gff3 file as an input for EVM ?
gtf braker2 gff3 tsebra
updated 2.2 years ago by 45k • written 2.5 years ago by • 0
2
votes
2
replies
6.7k
views
Guppy basecaller
NGS Linux nanopore Covid
updated 2.4 years ago by 45k • written 2.5 years ago by • 0
0
votes
2
replies
1.4k
views
How to analyze LINCS 1000 gz data
LINCS R
19 months ago by Md. Al - Mustanjid ▴ 30
0
votes
1
reply
761
views
Creating contaminated synthetic reads
Contaminated synthetic reads
updated 2.5 years ago by ★ 30k • written 2.5 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Remove multiple gene id from bed file
transcript bed genes
updated 2.4 years ago by 45k • written 2.5 years ago by • 0
0
votes
1
reply
1.1k
views
single-end read for scRNA-seq data
scRNA-seq 10X single-end
updated 2.5 years ago by 89k • written 2.5 years ago by ▴ 10
2
votes
6
replies
1.7k
views
problem with bedtools getfasta
getfasta bedtools
2.5 years ago by anasjamshed ▴ 140
3
votes
1
reply
1.0k
views
phred encoding issue in public dataset
phred fastq
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 40
0
votes
2
replies
1.1k
views
Find association between gene-mutation and cell count fold change
crispr mutation statistics gene
2.5 years ago by jason • 0
4
votes
1
reply
1.5k
views
Overlap File for RACON Genome Polisher
minimap2 overlap racon MHAP
updated 2.5 years ago by 3.9k • written 2.5 years ago by ▴ 50
1
vote
1
reply
780
views
Queuing jobs for a synthetic read generator python script
RQ Celery Multiprocessing. APScheduler Python
updated 2.5 years ago by 103k • written 2.5 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Comparing variant calls
bedtools VCF bcftools
updated 2.3 years ago by 45k • written 2.5 years ago by ▴ 110
2
votes
3
replies
1.2k
views
IPA analysis without FDR value column in the data sheet
IPA
2.5 years ago by FIS12 • 0
1
vote
3
replies
1.5k
views
".sam" file - should it contain multiple samples?
SAM
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 20
1
vote
2
replies
2.9k
views
Warning: [tblastn] Examining 5 or more matches is recommended
sma3s
2.5 years ago by Neel ▴ 20
8
votes
10
replies
3.5k
views
How to run STARsolo run over multiple samples like cellranger
cellranger starsolo
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 80
2
votes
4
replies
3.1k
views
Exon vs Transcript in featurecounts for RNA Seq
featurecounts rnaseq
2.5 years ago by murphytho1401 • 0
4
votes
1
reply
1.3k
views
DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values
geo geoquery microarray normalization deseq2
updated 2.5 years ago by 89k • written 2.5 years ago by ▴ 20
1
vote
1
reply
1.2k
views
heatmap color key
heatmap
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by ▴ 10
0
votes
0
replies
576
views
Struggling with protein context of Annovar output
protein context sequence R annovar
2.5 years ago by papp.benjamin.t • 0
6
votes
4
replies
6.3k
views
Creating binary matrix of absence/presence of genes in multiple column lists
upsetr R
updated 2.5 years ago by 12k • written 6.6 years ago by ▴ 20
48
votes
16
replies
6.8k
views
12 follow
Bio-Informatics Results Supporting Ongoing Evolution
evolution publication
written 14.8 years ago by ▴ 310
0
votes
0
replies
689
views
News: GWAS course in June
GWAS
updated 2.4 years ago by 45k • written 2.5 years ago by ★ 2.6k
3
votes
1
reply
914
views
How to get transcript coverage from Salmon output?
salmon RNAseq RSeQC transcriptome
updated 2.5 years ago by 103k • written 2.5 years ago by ▴ 60
0
votes
0
replies
572
views
How to extract P-Values and LogFC from lrTest in MAST?
MAST lrtest pvalue logFC
2.5 years ago by Tadeoye ▴ 30
2
votes
3
replies
1.2k
views
SKAT vs SIMES methods
pvalue gynotype SKAT simes R
updated 2.5 years ago by 5.1k • written 2.5 years ago by ▴ 40
0
votes
0
replies
1.7k
views
Job: Bioinformatics Research Scientist at CSU
github HPC R python
updated 2.4 years ago by 45k • written 2.5 years ago by • 0
0
votes
0
replies
650
views
multiple testing in 450K array data
minfi methylation 450K epigenetics statistics
2.5 years ago by eebloom ▴ 110
122,004 results • Page 268 of 2441
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Answer: How to create a consensus of a contig with samtools or bbmap?
Answer: How to create a consensus of a contig with samtools or bbmap?
Difficulty running FoldX in linux
Answer: Difficulty running FoldX in linux
Answer: Differences between published differential gene expression results and own analy
Answer: Differences between published differential gene expression results and own analy
Comment: Problems with PacBio's Improved Phased Assembler (IPA)
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Recent Replies
Answer: Recommendations for 200 SNP markers genotyping by Aleksandra ▴ 140
For a 200-SNP panel at your sample throughput, I would recommend an amplicon-based targeted sequencing approach. The workflow involves des…
Comment: Reasonable number of SNPs in a bacterial genome. by dthorbur ★ 3.1k
There are *a lot* of factors that can impact the number of identified SNPs. These include things like: - Evolutionary distance from samp…
Answer: DESeq2 on metagenome KO counts by Aleksandra ▴ 140
Your proposed workflow is indeed sound, as applying DESeq2 to KO-counts is perfectly valid; its underlying negative binomial model is metho…
Comment: Interpreting genomic features distribution for CUT&RUN peaks by Rozita ▴ 40
The massive difference has been reproducible across the 3 biological replicates and is in line with what we would expect in terms of the bi…
Answer: Interpreting genomic features distribution for CUT&RUN peaks by LChart 5.1k
My initial concern is the ~15-fold difference (450 vs 7500) between called peaks in the two different cell line conditions. This suggests t…
Comment: Recommendations for 200 SNP markers genotyping by Michael 56k
Which organism are you talking about, and are these markers fixed? You can search for existing genotyping options using this information. F…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by PolenP • 0
I tried Insilico seq as per your suggestion and it is really good. Unfortunately, it's taking more than 3 days to simulate 5x coverage of a…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
How did you get to these un-synced files? aka, what was your previous step in this analysis? I'm asking, as usually you need to make sure …
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Panos ★ 1.8k
Just so others know (in case they try) downgrading snakemake/python didn't work for me. In fact, I tried a number of different combinations…
Comment: headers missing in efetch results for SRA database by Leela • 0
Please note that this is still a problem in the recent version in `conda` (v24.0)
Comment: Difficulty running FoldX in linux by strayeroliver • 0
Thank you very much for your help.
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Billy Rowell ▴ 520
Completely understand. I hope this helps then!
Comment: Active site using castpfold by Mensur Dlakic ★ 30k
Please don't take my comment the wrong way. Docking ligands is a serious endeavor that includes many preparatory steps, a use of highly so…
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Panos ★ 1.8k
Thanks! I will try further downgrading snakemake (and python).. Actually, I have already tried `hifiasm` which worked perfectly (as always…
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
https://www.biostars.org/u/151541/ look through some of the top entries from this search for subread BAM's. Here is one example: https://do…
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