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931 results • Page 4 of 19
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5
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6
replies
543
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 9 days ago by ▴ 760 • written 10 days ago by ▴ 40
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 1 day ago by ▴ 10 • written 2.5 years ago by • 0
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 22 days ago by 43k • written 3.2 years ago by ▴ 170
4
votes
6
replies
515
views
Odd results with BLAST remote
blast remote NCBI
updated 23 days ago by ▴ 180 • written 24 days ago by ▴ 150
0
votes
6
replies
481
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 15 days ago by • 0 • written 5 weeks ago by ▴ 20
5
votes
5
replies
884
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 27 days ago by 43k • written 10 months ago by ▴ 30
2
votes
5
replies
762
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 18 days ago by ▴ 770 • written 20 days ago by ★ 2.4k
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 24 days ago by 43k • written 3.9 years ago by ▴ 250
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic Gene-Ontology GO
updated 28 days ago by 43k • written 2.1 years ago by • 0
0
votes
5
replies
417
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 12 days ago by 100k • written 15 days ago by ▴ 10
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 19 days ago by • 0 • written 6.5 years ago by ▴ 30
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 1 day ago by ▴ 90 • written 6.4 years ago by ▴ 60
1
vote
5
replies
646
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 19 days ago by 142k • written 20 days ago by • 0
0
votes
5
replies
218
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 1 day ago by 21k • written 1 day ago by • 0
0
votes
5
replies
262
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
1 day ago by me • 0
2
votes
5
replies
605
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 18 days ago by ★ 27k • written 19 days ago by • 0
3
votes
5
replies
615
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
17 days ago by n_navy • 0
1
vote
5
replies
1.6k
views
How to correct unknown Batch effect?
PCA gene-expression DESeq2 RNA-seq batch-effect
updated 22 days ago by 43k • written 12 months ago by ▴ 110
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 22 days ago by 43k • written 5.2 years ago by ★ 1.9k
0
votes
5
replies
334
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 hours ago by 22k • written 2 days ago by • 0
0
votes
5
replies
328
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 6 days ago by ▴ 20 • written 10 days ago by • 0
0
votes
5
replies
400
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
15 days ago by njornet ▴ 20
3
votes
5
replies
340
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
6 days ago by Maverick ▴ 10
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R RNA-Seq limma DE batch-effect
updated 22 days ago by 43k • written 4.8 years ago by ▴ 60
8
votes
5
replies
6.2k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
2
votes
5
replies
391
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
13 days ago by Lada ▴ 30
2
votes
5
replies
934
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 10 days ago by ★ 2.0k • written 2.1 years ago by • 0
4
votes
5
replies
419
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
10 days ago by analyst ▴ 50
1
vote
5
replies
630
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 16 days ago by • 0 • written 3 months ago by • 0
5
votes
5
replies
7.3k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 28 days ago by • 0 • written 3.8 years ago by ★ 1.8k
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 18 days ago by 43k • written 10.6 years ago by ▴ 150
5
votes
5
replies
285
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 7 days ago by ▴ 30 • written 7 days ago by ▴ 150
5
votes
5
replies
262
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
1 day ago by Chris ▴ 280
3
votes
5
replies
524
views
Having trouble building VG in Ubuntu
vg
updated 25 days ago by 43k • written 28 days ago by • 0
8
votes
5
replies
1.3k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 24 days ago by ▴ 210 • written 16 months ago by ★ 1.4k
0
votes
5
replies
371
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 6 days ago by ▴ 180 • written 7 days ago by • 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq countOverlaps R
updated 22 days ago by 43k • written 6.3 years ago by ★ 1.9k
2
votes
5
replies
513
views
Marking duplicates using UMIs
Deduplication UMI
updated 17 days ago by 19k • written 18 days ago by • 0
1
vote
5
replies
2.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 28 days ago by 82k • written 5.1 years ago by ▴ 750
0
votes
5
replies
391
views
Telescope issue
Telescope RNA-seq
updated 8 days ago by 142k • written 9 days ago by • 0
1
vote
5
replies
368
views
samtools filtering
samtools
updated 28 days ago by ★ 1.2k • written 5 weeks ago by ▴ 80
1
vote
5
replies
203
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 2 days ago by 19k • written 2 days ago by ★ 1.8k
1
vote
5
replies
784
views
RNA seq differential expression analysis
RNA-seq normalization
updated 20 days ago by ★ 1.7k • written 21 days ago by • 0
5
votes
5
replies
579
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 29 days ago by ▴ 580 • written 4 weeks ago by ▴ 40
0
votes
5
replies
418
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 14 days ago by 142k • written 15 days ago by ▴ 90
2
votes
5
replies
503
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
11 days ago by ashaneev07 ▴ 20
3
votes
5
replies
288
views
Generating mpileup file using samtools
mpileup samtools
updated 6 days ago by 21k • written 6 days ago by • 0
2
votes
5
replies
535
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
22 days ago by Bikram Kumar • 0
1
vote
5
replies
442
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
16 days ago by anasjamshed ▴ 120
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 1 day ago by • 0 • written 5.1 years ago by ★ 1.8k
931 results • Page 4 of 19
Recent Votes
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
cellranger error message
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Network plot from expression data in R using igraph
Comment: RNA seq analysis
RNA seq analysis
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Recent Replies
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length by marco.barr ▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length by marco.barr ▴ 100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message by Max • 0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s…
Comment: Different output for read length by marco.barr ▴ 100
Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis by s.ghazala • 0
Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 100
Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS by tim.booth ▴ 50
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile by tim.booth ▴ 50
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length by Pierre Lindenbaum 161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file by sainavyav22 • 0
Here you go. 1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput 2.perl annotate_variation.pl 100…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant. Your question is ambiguous because you…
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