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0 votes
8 replies
2.0K views
GCP Snakemake
snakemake gcp
updated by Ram Ram • written by Fadwa • Fadwa
5 votes
12 replies
34K views
Extract Alignment From Very Large Bam File
bam
updated by Ram Ram • written by Plantae Plantae
0 votes
1 reply
1.2K views
GATK-Pathseq validation
gatk
updated by Ram Ram • written by annaA • annaA
2 votes
3 replies
1.4K views
VEP classifies exonic variants as downstream
ensembl vep
updated by colindaven colindaven • written by tvrlisml • tvrlisml
0 votes
0 replies
617 views
unusual alignment rates for IgG and H3K27me3 in cuttag
bowtie2 cuttag
written by david • david
0 votes
3 replies
1.7K views
WGBS data presentation
wgbs r
updated by Binte.farooq • Binte.farooq • written by sinha.puja • sinha.puja
0 votes
6 replies
3.3K views
How to visualize multiple bacterial genomes with circos?
atlas genome visualization
updated by mathavanbioinfo mathavanbioinfo • written by marongiu.luigi marongiu.luigi
0 votes
1 reply
828 views
Differential Abundance between samples
differential-abundance mass-spectrometry
updated by i.sudbery i.sudbery • written by catfishtom • catfishtom
0 votes
4 replies
1.6K views
Suggestions for a simpler solution for collecting snakemake rule output in a text file for use in another rule?
snakemake
written by a.v.vliet • a.v.vliet
0 votes
6 replies
1.4K views
Doubt about fpkm file
fpkm rna-seq
updated by ATpoint ATpoint • written by mounavisirekolam • mounavisirekolam
1 vote
2 replies
904 views
Errors from REST and Browser for specific HOGS?
oma
written by Andrew • Andrew
0 votes
6 replies
2.2K views
Normal number of variants to lose during liftover: GRCh38 to hg19
liftover 1000genome crossmap
updated by Giulio Genovese • Giulio Genovese • written by JourneyToAbyss JourneyToAbyss
0 votes
1 reply
844 views
WGCNA - higher number of modules
wgcna
updated by allingt • allingt • written by marina.wakid • marina.wakid
0 votes
1 reply
960 views
mitch analysis report priority by standard deviation
mitch standard_deviation
updated by mark.ziemann mark.ziemann • written by Amr • Amr
0 votes
2 replies
1.2K views
How to get differntial Protein expression from protein abundance?
proteomics protein deps abundance
updated by Saadyeh • Saadyeh • written by Omar • Omar
0 votes
2 replies
1.3K views
Trouble Running VEP in Conda Environment Due to Perl DBD::mysql Error
perl conda vep
updated by Ram Ram • written by qiuting • qiuting
0 votes
6 replies
2.1K views
RNAseq analysis: how to add new gene into an existing worm based reference
rna-seq
updated by jkim • jkim • written by leranwangcs • leranwangcs
0 votes
7 replies
1.8K views
Iterate through Seurat object to add patient information
r seurat
updated by Ram Ram • written by kousi31 • kousi31
1 vote
5 replies
1.7K views
Annotation of Complex Heatmap
complexheatmap
written by abiuma • abiuma
0 votes
5 replies
2.6K views
Querying nr_clustered database using BLAST REST API?
blast clustered
updated by GenoMax GenoMax • written by cmdcolin cmdcolin
0 votes
1 reply
661 views
how to determine the percentage of reads after sequencing?
metagenomic sequencing
updated by GenoMax GenoMax • written by Ales • Ales
0 votes
1 reply
643 views
Error in GDCRNATools
gdcrnatools cerna rna-seq
written by Matvii Mykhailichenko • Matvii Mykhailichenko
1 vote
3 replies
1.2K views
WGCNA Soft Power Problem
normalization wgcna rna-seq deseq2
updated by LChart LChart • written by Ömür Koray • Ömür Koray
0 votes
0 replies
776 views
WGCNA module preservation
module-preservation wgcna
updated by Ram Ram • written by Gail • Gail
0 votes
2 replies
1.1K views
Docker container not running (or stopping immediately)
docker hi-c
updated by Eijy Nagai • Eijy Nagai • written by Panagiotis • Panagiotis
0 votes
2 replies
993 views
Alternatives to Mummer3 for linux?
alignmemt sequences aligner
updated by Dave Carlson Dave Carlson • written by marongiu.luigi marongiu.luigi
1 vote
1 reply
596 views
filtering gene sets when performing scRNAseq data analysis
scrna-seq
updated by Ram Ram • written by Sara Sara
0 votes
1 reply
694 views
Importing read pairs from BAM with specific R1 and R2 start/end positions for pair
rsamtools
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Emily Wasson • Emily Wasson
0 votes
0 replies
1.2K views
how convert a GraphPad PRISM parameters in R code?
r statistics regression
written by star star
0 votes
1 reply
960 views
Genome Analysis Insights: BUSCO Evaluation of Repetitive Elements and Ploidy Level in Crocus sativus"
coverage ploidy complex-genome busco
updated by Ram Ram • written by mathavanbioinfo mathavanbioinfo
0 votes
4 replies
2.2K views
Manhattan Plot
qqman pcadapt manhattan gwas
updated by dthorbur dthorbur • written by Emily • Emily
0 votes
2 replies
1.1K views
Need some help to develop some python code to analyze kmer data
python r
written by schlogl schlogl
0 votes
5 replies
2.0K views
Why do I get DE non-polyadenylated genes in a RNAseq with PoliA library?
lncrna polia dge rnaseq deseq2
updated by i.sudbery i.sudbery • written by ev97 • ev97
0 votes
1 reply
783 views
Analysis of .csv data in R software
tabe csv software data r
updated by ATpoint ATpoint • written by martta95 • martta95
1 vote
3 replies
2.7K views
GOSeq gene ontology enrichment analysis in rice
goseq r
updated by i.sudbery i.sudbery • written by Bioinfonext Bioinfonext
0 votes
1 reply
959 views
Batch correction for eQTL analysis
batch eqtl batch-correction batch-effect
updated by Ram Ram • written by maximal_life • maximal_life
0 votes
1 reply
900 views
how convert hg19 to hg38
hg19 hg38
updated by Pierre Lindenbaum Pierre Lindenbaum • written by arwa.ahmad95 • arwa.ahmad95
0 votes
0 replies
462 views
Obtain expression data for the specific genes on integrated seurat project
scrna-seq seurat
written by gdfsnkfns • gdfsnkfns
0 votes
4 replies
1.8K views
Trouble with samtools view not filtering specified regions of bam file
bam samtools
updated by Istvan Albert Istvan Albert • written by haydenshinn • haydenshinn
0 votes
0 replies
1.2K views
Tool: Get `BPCells` with Bioconductor workflow
single cell bpcells
written by Yun • Yun
0 votes
15 replies
3.4K views
I would like to exclude rRNA in RSEM and quantify other genes.
star rna-seq rsem
updated by dsull dsull • written by Apprentice Apprentice
0 votes
7 replies
5.0K views
Help in choosing the right metric for ranking genes in fgsea
fgsea gsea
written by Ngrin • Ngrin
0 votes
9 replies
1.9K views
Approach for multi species comparative transcriptomics and differential expression analyses
de rna-seq transcriptomics
updated by dthorbur dthorbur • written by fish_enthusiast • fish_enthusiast
0 votes
7 replies
4.0K views
Downstream analysis from STAR Alignment at transcript level
star isoformswitchanalyzer transcript-level deseq2 salmon
updated by Zhihao • Zhihao • written by bassanio • bassanio
0 votes
0 replies
981 views
trying to upgrade from Bio.pairwise2.align to Bio.Align
pairwise2 bio.align python biopython
updated by Ram Ram • written by Richard • Richard
0 votes
4 replies
1.2K views
Values EXCEEDS the original data range after batch effect correction.
batch-effect limma
updated by Ram Ram • written by Mary • Mary
0 votes
3 replies
1.0K views
learning bioinformatics
course learning
updated by Ram Ram • written by sevda • sevda
0 votes
8 replies
2.3K views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
phobius
updated by ido.idobar • ido.idobar • written by Elizabeth • Elizabeth
0 votes
0 replies
928 views
Understanding Homer output for makeTagDirectory
chip-seq peaks homer maketagdirectory
written by Assa Yeroslaviz Assa Yeroslaviz
0 votes
2 replies
2.0K views
Create Signature Matrix Cibersort
cibersort
written by Nona • Nona
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