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569 results • Page 3 of 12
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0
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4
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2.1k
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picard markduplicate output smaller file
picard markduplicates gatk
updated 11 days ago by 39k • written 4.4 years ago by ▴ 190
2
votes
4
replies
823
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python biopython
updated 1 day ago by 39k • written 3.6 years ago by • 0
2
votes
4
replies
610
views
DESeq2 batch effects with nonuniform design matrix
DESeqDataSet DESeq2 batch
updated 25 days ago by 39k • written 12 months ago by ▴ 20
0
votes
4
replies
1.3k
views
How can I extract position information from multiple alignment format?
CLUSTAL MAFFT multiple-alignment
updated 21 days ago by 39k • written 3.3 years ago by • 0
1
vote
4
replies
4.9k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R heatmap
updated 18 days ago by 39k • written 5.3 years ago by ▴ 60
3
votes
4
replies
3.8k
views
What are the Pros and Cons of working in Bioinformatics???
career bio
updated 18 days ago by 39k • written 5.3 years ago by ▴ 20
4
votes
4
replies
293
views
Does adding reads cause batch effects?
kallisto RNAseq
updated 5 days ago by 72k • written 5 days ago by ▴ 80
0
votes
4
replies
201
views
Difference between USCS exon coordinates and ensembl
exons Ensembl
1 day ago by amy__ ▴ 50
1
vote
4
replies
224
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf UCSC PHAST multiz
1 day ago by Daniel ▴ 30
0
votes
4
replies
336
views
csv to custom manifest file
illumina
26 days ago by bioguy24 ▴ 230
1
vote
4
replies
2.3k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment msa alignment
updated 21 days ago by 39k • written 7.1 years ago by ▴ 260
0
votes
4
replies
279
views
Identification of genes involved in my pathway
KEGG keggGet
5 days ago by smanzano250800 • 0
1
vote
4
replies
273
views
My VCF file structure is strange and less compatible to data processing programs.
VCF GATK SNPs
updated 27 days ago by 98k • written 27 days ago by • 0
0
votes
4
replies
484
views
BBduk reading fastq from S3 directly - Is it possibile?
BBduk BBTools BBMap
16 days ago by Marko ▴ 10
0
votes
4
replies
3.7k
views
What is Dunn's multiple comparison test?
statistics
updated 21 days ago by 39k • written 5.8 years ago by • 0
1
vote
4
replies
559
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx differential-expression t-test deconvolution
updated 25 days ago by 72k • written 5 weeks ago by ▴ 280
0
votes
4
replies
281
views
To match fragments within range - Python or awk
awk python
27 days ago by L_bioinfo • 0
0
votes
4
replies
293
views
I need help with a methyl array data analysis
methyl_array DMPs DMRs beta_value r
9 days ago by Ahmad ▴ 10
0
votes
4
replies
521
views
From VCF to BEAGLE format with multiple chromosomes
vcf vcftools beagle gvcf
14 days ago by Begonia_pavonina ▴ 100
2
votes
4
replies
1.3k
views
hisat2 SyntaxError: invalid syntax
alignment hisat2
updated 22 days ago by 39k • written 19 months ago by ▴ 10
0
votes
4
replies
791
views
Detecting Biomarkers from Time Series Gene Epression data
Time-Series Gene-Expression Biomarkers
updated 7 days ago by 39k • written 3.2 years ago by • 0
0
votes
4
replies
5.0k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 1 day ago by • 0 • written 5.6 years ago by ▴ 30
0
votes
4
replies
4.8k
views
Sequence alignment length
multiple-sequence-alignment
updated 21 days ago by 39k • written 6.3 years ago by ▴ 20
0
votes
4
replies
1.1k
views
No space separating sequence and name PopArt error !?
popart traits haplotypes python
updated 25 days ago by 39k • written 2.1 years ago by • 0
1
vote
4
replies
2.5k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl ortho ubuntu mysql
updated 13 days ago by 39k • written 5.0 years ago by ▴ 20
3
votes
4
replies
634
views
R package DESeq2 in R 3.5.1
R
updated 26 days ago by 39k • written 5 months ago by • 0
2
votes
4
replies
239
views
Filter VCF file for variant alleles
VCF variants bcftools vcftools
updated 6 days ago by 39k • written 6 days ago by • 0
0
votes
4
replies
273
views
Detect mutations in clonally propagated plants
mutations Illumina clonal-propagation variant-calling
26 days ago by RvV ▴ 10
2
votes
3
replies
276
views
Using RNA-seq to detect pathogen sequences in host tissue
RNA-seq
13 days ago by erik.burchard ▴ 10
1
vote
3
replies
1.4k
views
Is there any tool available for sequence alignment concatenation and supermatrix file generation other than Fastconcat-G?
Assembly alignment software-error
updated 1 day ago by 39k • written 3.6 years ago by ▴ 100
0
votes
3
replies
1.5k
views
Converting a mutation data file into vcf?
next-gen-sequencing exome
updated 25 days ago by 39k • written 6.0 years ago by ▴ 20
2
votes
3
replies
343
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
27 days ago by Dan ▴ 120
0
votes
3
replies
180
views
DEGseq for multiple samples
DEGseq DEG
updated 5 days ago by 39k • written 6 days ago by • 0
0
votes
3
replies
359
views
Picard ribosome intervals list
Picard
18 days ago by mropri ▴ 140
1
vote
3
replies
621
views
miRDeep2.pl error in make_html2.pl
miRNA mirDeep make_html2.pl
updated 22 days ago by 39k • written 21 months ago by • 0
1
vote
3
replies
598
views
What is the best approach to detect unknown recombinant gene in genome?
recombinant sequencing
updated 18 hours ago by 39k • written 3.4 years ago by ▴ 240
3
votes
3
replies
483
views
[bwa_aln_core] calculate SA coordinate... script.sh: line 91: 183402 Killed
HPC BWA Alignment
updated 25 days ago by 39k • written 16 months ago by ▴ 20
0
votes
3
replies
2.9k
views
From FASTQ to clean BAM using GATK tutorial #6484
gatk MergeBamAlignment uBAM bamclipper
updated 20 days ago by 39k • written 5.6 years ago by ▴ 220
1
vote
3
replies
242
views
Where to upload and store annotated genetic variant data online?
mutation annotated cancer database variant
updated 21 days ago by 129k • written 22 days ago by ▴ 20
0
votes
3
replies
1.4k
views
SNPEff not showing SNP
snpEff variant-annotation SNP
updated 15 days ago by 39k • written 5.1 years ago by • 0
0
votes
3
replies
1.2k
views
Ensemble file Mus_musculus.GRCm38.dna.primary_assembly.fa.gz unzipping to incorrect contents
genome RSEM Ensembl
updated 22 days ago by 39k • written 19 months ago by ▴ 10
1
vote
3
replies
55
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence genome prediction masking
updated 16 minutes ago by 4.4k • written 3 hours ago by • 0
1
vote
3
replies
585
views
Is it wrong to use only a random subset of a dataset?
ethics research dataset
updated 25 days ago by 39k • written 17 months ago by ▴ 110
1
vote
3
replies
349
views
Variant calling analysis
vcf variant-calling wgs
updated 15 days ago by 9.6k • written 16 days ago by • 0
0
votes
3
replies
2.4k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly genome
updated 4 days ago by 39k • written 3.7 years ago by • 0
1
vote
3
replies
333
views
Retrieve Promoter Sequences by GeneID
GeneID by Sequences Retrieve Promoter
updated 15 days ago by 14k • written 5 weeks ago by • 0
0
votes
3
replies
230
views
Query qbout single cell sequencing
fastq ScRNA
updated 7 days ago by 39k • written 9 days ago by ▴ 20
1
vote
3
replies
999
views
BLAST: overflow error
BLAST
updated 25 days ago by 39k • written 13 months ago by ▴ 50
1
vote
3
replies
221
views
To call variants can I use my aligned WGS data as a reference genome
VCF samtools reference genome
updated 6 days ago by 129k • written 6 days ago by • 0
0
votes
3
replies
561
views
Problem with SHAPEIT
SHAPEIT
updated 25 days ago by 39k • written 10 months ago by • 0
569 results • Page 3 of 12
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: DESeq2 for different design and normalized counts by ATpoint 72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by ATpoint 72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values by ATpoint 72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments by Alexander ▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
Thanks a lot, it works
Comment: Differential protein expression analysis by dsull ★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis by Ribo ▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Answer: Extract sequences from a fastq file by a list of IDs by GenoMax 129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. The `counts` is log2-normalized raw data.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Ayish • 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix? by Thu • 0
Hi! Thanks for sharing your solution! It works! :)
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