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122,211 results • Page 699 of 2445
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12
votes
8
replies
7.5k
views
Is there a way to visualize log fold changes for Reactome pathways in R?
pathview RNA-Seq reactome bioconductor
updated 4.7 years ago by ▴ 440 • written 6.6 years ago by ▴ 180
0
votes
1
reply
1.2k
views
Is there any way to access the --cores argument in a snakemake workflow?
snakemake
updated 3.9 years ago by ▴ 190 • written 4.7 years ago by ▴ 900
2
votes
2
replies
1.0k
views
Sequencing Information from BAM file
RNA-Seq BAM alignment Library
4.7 years ago by MarVi ▴ 30
8
votes
10
replies
2.4k
views
Performing Differential expression analysis using DESeq with 3 conditions
RNA-Seq Deseq2 R next-gen bioconductor
4.7 years ago by bionewbie • 0
0
votes
2
replies
1.0k
views
Identifiying SNP frequencies for very specific subpopulations on dbSNP
SNP
4.7 years ago by Michael ▴ 290
3
votes
3
replies
2.5k
views
Counts alongside Fold changes - FindMarkers Seurat
RNA-Seq seurat
4.7 years ago by ishwariyavenkatesh • 0
0
votes
0
replies
656
views
Statistical correlation for in-group vs outgroup trait frequencies
statistics p-value spearman correlation
4.7 years ago by leonid.rusin • 0
0
votes
0
replies
663
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
updated 4.7 years ago by 20 • written 4.7 years ago by • 0
2
votes
1
reply
1.5k
views
plink --indep LD calculation and filtering to VCF file in one command
plink
4.7 years ago by rjzotti • 0
1
vote
6
replies
3.5k
views
Setting genotypes to missing for certain positions in vcf file
vcf vcftools
updated 4.7 years ago by 166k • written 4.7 years ago by • 0
6
votes
3
replies
12k
views
The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
sequence genome
updated 4.7 years ago by ▴ 20 • written 5.9 years ago by ▴ 320
3
votes
2
replies
4.6k
views
Can't create tabix index of the bed file
samtools tabix bed ATAC-seq
updated 4.7 years ago by ▴ 290 • written 4.7 years ago by ▴ 10
0
votes
5
replies
1.4k
views
Shrunk data from Novogene
RNA-Seq
4.7 years ago by Futuremaking • 0
1
vote
2
replies
1.7k
views
scRNA cross-species integration using Seurat v3
integration scRNA-Seq FindIntegrationAnchors
4.7 years ago by maddhesiya13 • 0
5
votes
8
replies
2.6k
views
A layman trying to understand what a FASTA file is
RNA-Seq gene next-gen-sequencing
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 40
0
votes
3
replies
1.9k
views
change missing genotype in bcf file from 0/0 to ./. to run plink
bcftools plink SNP genotype bcf
4.7 years ago by rah ▴ 30
0
votes
1
reply
2.9k
views
BLAST error: Input db vol size does not match lmdb vol size
BLAST Database Error Protein NR
4.7 years ago by Hansen_869 ▴ 80
3
votes
3
replies
1.5k
views
installation of shovill on windows
software error assembly
updated 4.7 years ago by ▴ 90 • written 4.7 years ago by ▴ 20
0
votes
22
replies
4.5k
views
Specifying database path in BLAST standalone
blast path standalone
4.7 years ago by Hansen_869 ▴ 80
0
votes
0
replies
966
views
Plasmids in the Resfinder tool?
resfinder sequencing antibiotic resistance
4.7 years ago by Researcher ▴ 20
1
vote
1
reply
1.2k
views
CWL workflow - nested_crossproduct output
CWL scatter workflow nested_crossproduct
updated 4.4 years ago by ★ 1.9k • written 4.7 years ago by ▴ 300
2
votes
4
replies
1.3k
views
featurecounts -p Paried ends which count total to use as read1 &read 2 give different totals.
RNA-Seq alignment R gene sequencing
4.7 years ago by ray.liv.wong • 0
3
votes
3
replies
1.2k
views
How can the assumption of a broad/narrow peak be checked?
macs2 ChIP-Seq
4.7 years ago by Aspire ▴ 390
1
vote
1
reply
1.1k
views
variant calling using masked reference genome
Bowtie2 Reference Genome Variant Calling
4.7 years ago by reza ▴ 300
7
votes
11
replies
4.6k
views
What is the appropriate approach for ChIPseq protein genome occupancy % calculation?
ChIP-Seq
updated 2.9 years ago by 45k • written 10.4 years ago by ▴ 120
4
votes
18
replies
5.2k
views
Want to reverse the fasta sequence
fasta
4.7 years ago by harry ▴ 40
2
votes
4
replies
3.4k
views
Read VEP output from command line in R
vep ensembl R Bash
updated 16 months ago by • 0 • written 4.7 years ago by ▴ 100
1
vote
2
replies
977
views
In-silico downsizing to estimate the DNA input
sequencing snp next-gen
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 40
0
votes
6
replies
1.0k
views
How to get related proteins and gene data of an organism (for eg. Lactobacillus )
gene genome
updated 4.7 years ago by 22k • written 4.7 years ago by • 0
3
votes
6
replies
5.7k
views
Is the ENSEMBL FTP down?
ensembl ftp
updated 4.2 years ago by ▴ 940 • written 4.7 years ago by ★ 1.5k
0
votes
1
reply
1.0k
views
Kraken abundances do not add up
kraken2
4.7 years ago by jsgounot ▴ 170
1
vote
1
reply
3.6k
views
Suggest vcf filtered parameter for gatk VariantFiltration
gatk4 snps
updated 4.7 years ago by ▴ 160 • written 6.5 years ago by ▴ 140
0
votes
0
replies
817
views
Run TSS predator without TEX wig libraries
RNA-Seq sequencing next-gen software error
4.7 years ago by qstefano ▴ 20
0
votes
1
reply
1.3k
views
Repeated measures in GWAS and polygenic risk scores analyses
SNP
updated 2.1 years ago by 12k • written 5.7 years ago by ▴ 20
0
votes
2
replies
2.0k
views
conversion of a genlight object into a genpop object
snp R
updated 2.4 years ago by • 0 • written 5.3 years ago by • 0
0
votes
1
reply
2.7k
views
KEGG Reconstruct Pathway: More Efficient Usage
Kegg Pathway genome
updated 4.7 years ago by 20 • written 8.3 years ago by • 0
1
vote
2
replies
1.4k
views
Data normalization (raw counts) and DEG analysis. Do I have a problem with my pipeline?
R RNA-Seq
4.7 years ago by Peter ▴ 20
0
votes
0
replies
1.1k
views
Is it possible to call variants using cram files?
next-gen sequencing SNP
4.7 years ago by vinayjrao ▴ 260
32
votes
34
replies
19k
views
10 follow
How To Randomly Sample A Subset Of Lines From A Bed File
bed chip-seq
updated 4.1 years ago by 45k • written 12.1 years ago by ▴ 540
1
vote
3
replies
3.9k
views
Meme/Ame - bad file error
meme ame motif
4.7 years ago by LacquerHed ▴ 30
6
votes
8
replies
2.2k
views
What does mean HHHHHH in structures?
structure protein pdb
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 80
0
votes
1
reply
2.5k
views
ERROR UTR only implemented with shadow and partial or complete. Augustus
busco Augustus
updated 4.7 years ago by ▴ 80 • written 5.6 years ago by • 0
5
votes
2
replies
1.1k
views
NCBI genome stats
genome stats ncbi
updated 4.7 years ago by 154k • written 4.7 years ago by ★ 2.0k
0
votes
0
replies
1.1k
views
gromacs: RNA-Protein interaction
gromacs RNA Protein
updated 4.7 years ago by 20 • written 4.9 years ago by ▴ 10
4
votes
10
replies
2.9k
views
Importing quant.sf file to tximport
software-error tximport genome
updated 2.5 years ago by 45k • written 4.7 years ago by • 0
2
votes
2
replies
2.1k
views
Deleting text from row.names in a dataframe
RNA-Seq
4.7 years ago by salehm ▴ 10
0
votes
1
reply
1.2k
views
Docker image exceRpt pipeline help
docker small RNA seq RNAseq exceRpt
updated 4.7 years ago by ▴ 320 • written 4.7 years ago by • 0
3
votes
3
replies
2.0k
views
How to concatenate multiple fastq files (located in different directories) for each sample
RNA-Seq
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 10
0
votes
6
replies
2.0k
views
Running PHG with singularity: Error at CreatePHG_step2_addHapsFromGVCF
PHG singularity
4.7 years ago by bp • 0
2
votes
2
replies
1.5k
views
chr20_KI270871v1_alt in HG38 Broad Variant and Blacklist regions
ChIP-Seq
4.7 years ago by ahadli.farid ▴ 50
122,211 results • Page 699 of 2445
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Recent Replies
Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 130
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
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