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187 results • Page 1 of 4
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6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 6 days ago by • 0 • written 6.5 years ago by ▴ 130
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
5 days ago by vytarasov ▴ 180
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 5 days ago by • 0 • written 5.7 years ago by ▴ 20
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq alignment RNA-Seq featureCounts STAR
updated 3 days ago by ▴ 340 • written 4.9 years ago by ▴ 70
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 6 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 11 hours ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by • 0 • written 7.1 years ago by • 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 3 days ago by • 0 • written 5.1 years ago by • 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by • 0 • written 4.8 years ago by ▴ 60
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 4 days ago by • 0 • written 6.7 years ago by • 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11 Autodock windows MGLTools
updated 2 days ago by 43k • written 13 months ago by • 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 1 day ago by 43k • written 3.9 years ago by • 0
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
2 days ago by Arton ▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython FASTA
updated 3 days ago by • 0 • written 2.6 years ago by • 0
1
vote
3
replies
794
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 16 hours ago by ▴ 90 • written 2.7 years ago by ▴ 80
1
vote
5
replies
785
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
2
votes
9
replies
694
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 days ago by 161k • written 9 days ago by • 0
2
votes
11
replies
608
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
3 hours ago by egascon • 0
0
votes
9
replies
598
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
1 day ago by Arton ▴ 10
1
vote
14
replies
597
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
5 hours ago by hophuquy0944 • 0
0
votes
9
replies
596
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 1 day ago by ★ 2.0k • written 10 days ago by ▴ 140
2
votes
5
replies
567
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 4 days ago by ▴ 40 • written 13 days ago by ▴ 30
0
votes
1
reply
543
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq QC single cell BDRhapsody analysis
updated 1 day ago by ▴ 20 • written 12 months ago by • 0
0
votes
11
replies
533
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
4 days ago by Tuck898 • 0
0
votes
1
reply
531
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
updated 4 days ago by ▴ 300 • written 27 days ago by • 0
1
vote
4
replies
499
views
cellranger error message
multiplexing cellranger
updated 6 days ago by • 0 • written 3 months ago by ▴ 10
2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 2 days ago by 43k • written 8 days ago by • 0
3
votes
6
replies
489
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 days ago by ▴ 20 • written 11 days ago by • 0
5
votes
7
replies
485
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
1
vote
3
replies
432
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
3 days ago by kalavattam ▴ 190
0
votes
7
replies
427
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 4 days ago by ▴ 20 • written 18 days ago by • 0
0
votes
2
replies
425
views
News: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq variant-calling RNA-seq illumina transcriptomics
3 days ago by David Langenberger 11k
0
votes
6
replies
419
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 3 days ago by 43k • written 6 days ago by • 0
1
vote
4
replies
412
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 6 days ago by 142k • written 29 days ago by • 0
4
votes
7
replies
403
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
0
votes
4
replies
397
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by beginner123 • 0
1
vote
9
replies
392
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 6 days ago by 19k • written 9 days ago by ★ 1.8k
6
votes
7
replies
385
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
1
vote
7
replies
380
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
2 days ago by ntsopoul ▴ 60
2
votes
6
replies
380
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
2
votes
8
replies
375
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 4 days ago by 161k • written 5 days ago by ▴ 100
1
vote
2
replies
358
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq limma RNA-seq removeBatchEffect batch-effect
updated 3 days ago by 43k • written 4 days ago by • 0
3
votes
3
replies
358
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 3 days ago by ▴ 140 • written 6 days ago by • 0
0
votes
3
replies
352
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
3 days ago by mropri ▴ 150
0
votes
9
replies
342
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
1 day ago by njornet ▴ 20
0
votes
3
replies
342
views
Snakemake wrapper issue
fastqc snakemake
updated 3 days ago by • 0 • written 9 weeks ago by • 0
1
vote
4
replies
341
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 2 days ago by 8.6k • written 3 days ago by ▴ 30
1
vote
4
replies
339
views
Contig assembly task, errors
dna genetics contig assembly
updated 3 days ago by 43k • written 8 days ago by • 0
3
votes
4
replies
334
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 22 hours ago by 142k • written 1 day ago by 161k
0
votes
5
replies
330
views
How to convert normalized BigWig file to count matrix?
count-matrix BigWig
4 days ago by feather-W • 0
187 results • Page 1 of 4
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Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 10
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 10
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index by Lorenzo • 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto by dariober 14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err by GenoMax 142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem by Pierre Lindenbaum 161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by DGTool ▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
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