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1,000 results • Page 5 of 20
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3
votes
7
replies
7.8k
views
RNA-STAR, mapping problem (number of reads)
RNA-Seq
updated 21 months ago by 43k • written 8.2 years ago by • 0
5
votes
5
replies
7.8k
views
How can I get FastQC html report?
fastqc NGS fastqc error fastqc report
updated 7.6 years ago by 7.5k • written 7.6 years ago by ▴ 70
4
votes
45
replies
7.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 13 months ago by 43k • written 7.9 years ago by ▴ 110
4
votes
12
replies
7.8k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 12 weeks ago by ▴ 10 • written 3.4 years ago by ▴ 60
2
votes
10
replies
7.8k
views
fq.gz file use
BioEdit R
updated 13 months ago by 43k • written 5.2 years ago by • 0
1
vote
1
reply
7.8k
views
Large number of Unassigned_NoFeature reads from featureCounts
RNA-Seq featureCounts tophat2 unassigned counts
7.0 years ago by price0416 ▴ 10
0
votes
10
replies
7.8k
views
Error: reads file does not look like a fastq file
fastq bowtie2 ChIP-Seq
updated 13 months ago by 43k • written 7.6 years ago by ▴ 40
3
votes
5
replies
7.8k
views
Visualising the number of overlapping peaks in ChIP-seq studies
ChIP-Seq
updated 21 months ago by 43k • written 8.2 years ago by ★ 3.4k
1
vote
13
replies
7.8k
views
makeblastdb doesn't create database output
makeblastdb blast fasta NCBI blast+
updated 7.0 years ago by 141k • written 7.0 years ago by ▴ 50
0
votes
1
reply
7.7k
views
Merge VCF files using PLINK with repetition of the same VCF file for more than one individual
plink vcf vcftools
updated 6.6 years ago by 20 • written 6.7 years ago by • 0
2
votes
4
replies
7.7k
views
BLAST parameters and explanation
assembly gene alignment sequence genome
updated 5.6 years ago by 47k • written 5.6 years ago by ▴ 50
4
votes
3
replies
7.6k
views
How to plot variables in ggplot2 based on color by value
R ggplot2 geom_point variable dataframe
4.3 years ago by mohammedtoufiq91 ▴ 250
9
votes
27
replies
7.6k
views
How do I use Glimmer 3.02?
sequencing
updated 5.3 years ago by • 0 • written 6.1 years ago by ▴ 50
0
votes
10
replies
7.6k
views
Multiple paired-end gzipped fastq files as input into hisat2 error - fastq format not recognised
RNA-Seq hisat2 fastq gzip list input
7.6 years ago by nwon ▴ 60
1
vote
1
reply
7.6k
views
Needleman Wunsch algorithm coding in python for global alignment
python global alignment algorithm needleman wunsch
6.0 years ago by hbleed121 ▴ 10
1
vote
3
replies
7.6k
views
How to normalize median-center log-transform an expression matrix
R RNA-Seq
5.4 years ago by user31888 ▴ 130
2
votes
5
replies
7.6k
views
RNA seq analysis using STAR+StringTie
rna-seq STAR StringTie
7.3 years ago by fatima • 0
2
votes
9
replies
7.6k
views
6 follow
Read MAP and PED files in PLINK
GWAS PLINK
updated 4 months ago by 141k • written 6.0 years ago by • 0
4
votes
3
replies
7.6k
views
How To Smooth Ecdf Plot
10.2 years ago by Chirag Nepal ★ 2.4k
5
votes
2
replies
7.6k
views
DESeq2 log2 fold change
Nanostring deseq2
5.7 years ago by bioinfonerd ▴ 80
1
vote
2
replies
7.6k
views
Converting vcf to fasta format
fasta samtools vcf alignment next-gen
updated 16 months ago by 43k • written 8.9 years ago by ▴ 10
4
votes
8
replies
7.6k
views
GO term enrichment analysis using DAVID: How to start data analysis?
GO term enrichment DAVID GO Slim Bar graph Yeast
8.1 years ago by Curie ▴ 20
2
votes
7
replies
7.6k
views
Bowtie2 run out of memory
software-error alignment bowtie2
updated 15 months ago by 43k • written 9.0 years ago by ▴ 50
2
votes
28
replies
7.5k
views
Memory use in indexing
Assembly software error
updated 5.7 years ago by 43k • written 5.9 years ago by ▴ 710
0
votes
5
replies
7.5k
views
Export coverage Track from IGV
igv bedtools depth genomecov
6.0 years ago by MarVi ▴ 30
0
votes
9
replies
7.5k
views
How to calculate RPM (reads per million mapped reads)?
RNA-Seq
updated 4.3 years ago by 20 • written 7.2 years ago by ▴ 50
5
votes
3
replies
7.5k
views
reading gse series matrix data
python
4.8 years ago by cs18s003 ▴ 20
2
votes
6
replies
7.5k
views
Python Help: Plots are not appearing in the Spyder Console
Python Omics
4.7 years ago by WUSCHEL ▴ 750
5
votes
4
replies
7.5k
views
Bwa Installation Failed After "Make" Command In Linux
bwa
updated 10.7 years ago by 100k • written 10.7 years ago by ▴ 310
1
vote
9
replies
7.5k
views
SCTransform prior or after merging samples into one object?
Seurat scRNAseq merging samples
updated 2.1 years ago by ▴ 850 • written 3.6 years ago by • 0
3
votes
3
replies
7.5k
views
BS-seq: Using single end vs paired end in Bismark when Mapping efficiency is low
alignment bisulfite bismark methylation
updated 7.2 years ago by 20 • written 7.7 years ago by ▴ 70
5
votes
22
replies
7.5k
views
SVM for classified gene expression data
R svm microarray
updated 21 months ago by 43k • written 8.3 years ago by ▴ 50
4
votes
5
replies
7.5k
views
Understanding subsampling with Samtools
RNA-Seq subsampling samtools seed reads
updated 2.8 years ago by ▴ 850 • written 5.7 years ago by ▴ 420
2
votes
6
replies
7.5k
views
Install Bowtie2 on Windows 10 Home edition
genome next-gen sequencing software error
updated 6.4 years ago by 141k • written 6.4 years ago by ▴ 80
6
votes
4
replies
7.5k
views
vcftools Warning: Expected at least 2 parts in FORMAT entry
vcftools
4.9 years ago by Zoey Zou ▴ 70
3
votes
8
replies
7.5k
views
What are lowercase a,t,c,g refer to in a complete genome? Should lower case a,t,c,g to be converted to uppercase A,T,C,G before simulation?
genome Assembly
7.2 years ago by saranpons3 ▴ 70
0
votes
5
replies
7.4k
views
How to create publication quality figures in vector scale format
DS visualizer Ligplus figure
updated 5.1 years ago by 161k • written 5.1 years ago by • 0
4
votes
7
replies
7.4k
views
How to create chain file to change genome coordinates from one genome version to another
remap liftover chain-format
updated 2.2 years ago by 43k • written 9.6 years ago by 6.2k
1
vote
1
reply
7.4k
views
IGV Could not create index file when loading GFF3
IGV GFF3
7.0 years ago by emurb ▴ 10
5
votes
3
replies
7.4k
views
EdgeR without replicate?
RNA-Seq edgeR Corset differential'
4.6 years ago by 1234anjalianjali1234 ▴ 50
3
votes
3
replies
7.4k
views
BWA and Soft clipping
alignment genome sequencing
7.5 years ago by christopher.patterson3 • 0
1
vote
3
replies
7.4k
views
Sliding Window Ka/Ks (Dn/Ds) Analysis Via Python?
evolution protein
10.3 years ago by a1ultima ▴ 840
0
votes
2
replies
7.4k
views
How to use MACS2 to do peak calling
ChIP-Seq
updated 5.8 years ago by 20 • written 5.9 years ago by ▴ 120
0
votes
2
replies
7.4k
views
conversion of ensembl to gene_symbol in seurat
Seurat conversion spatial transcriptome
2.4 years ago by Omics data mining ▴ 260
1
vote
1
reply
7.4k
views
Multiple sequence alignment between multi fasta files ?
msa alignments
updated 3.1 years ago by 43k • written 9.2 years ago by 12k
0
votes
3
replies
7.4k
views
The Problem of Computing FPKM by DESeq2
RNA-Seq R
6.1 years ago by gengyang12138 ▴ 20
0
votes
2
replies
7.4k
views
Problems with PLINK on Mac OS X
Plink Mac OSX
updated 7.8 years ago by 20 • written 8.0 years ago by • 0
2
votes
6
replies
7.3k
views
PLINK returns NA values for all minor allele frequencies in my data
freq plink maf SNP
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 60
1
vote
5
replies
7.3k
views
How To Create Cluster Files For Plink When Performing A Stratified Analysis On Three Different Population Datasets
deleted-post
updated 11.1 years ago by 100k • written 11.1 years ago by ▴ 960
1
vote
10
replies
7.3k
views
BLAST memory usage
blast
updated 2.8 years ago by ▴ 50 • written 7.5 years ago by ▴ 10
1,000 results • Page 5 of 20
Recent Votes
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Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
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Recent Replies
Comment: Post-imputation plot by kl ▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis by GenoMax 141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems by ATpoint 82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot by LChart 3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq by Adam ▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject by Adam ▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems by Adam ▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis by GenoMax 141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long by bkleiboeker ▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue by GenoMax 141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery by GenoMax 141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue by eleven11 • 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems by Ram 43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
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