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183 results • Page 1 of 4
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38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 6 hours ago by ▴ 170 • written 7.1 years ago by ▴ 240
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
6 days ago by vytarasov ▴ 180
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 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 4 days ago by ▴ 340 • written 4.9 years ago by ▴ 70
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 23 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
3.0k
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 5 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 3 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 2 days 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
5
replies
798
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
1
vote
3
replies
797
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 1 day ago by ▴ 90 • written 2.7 years ago by ▴ 80
2
votes
9
replies
695
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 days ago by 161k • written 10 days ago by • 0
2
votes
11
replies
650
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
14 hours ago by egascon • 0
1
vote
14
replies
618
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
16 hours ago by hophuquy0944 • 0
0
votes
9
replies
602
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 2 days ago by ★ 2.0k • written 11 days ago by ▴ 140
0
votes
9
replies
599
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
2 days ago by Arton ▴ 10
2
votes
5
replies
568
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 5 days ago by ▴ 40 • written 14 days ago by ▴ 30
0
votes
1
reply
558
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
535
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
5 days ago by Tuck898 • 0
0
votes
1
reply
535
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 28 days ago by • 0
2
votes
5
replies
493
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 3 days ago by 43k • written 9 days ago by • 0
5
votes
7
replies
489
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
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 12 days ago by • 0
4
votes
7
replies
436
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 9 hours ago by ▴ 130 • written 2 days ago by ▴ 20
0
votes
7
replies
435
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
1
vote
3
replies
434
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
4 days ago by kalavattam ▴ 190
0
votes
2
replies
430
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
4 days ago by David Langenberger 11k
0
votes
6
replies
421
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 4 days ago by 43k • written 6 days ago by • 0
4
votes
7
replies
412
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
401
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by beginner123 • 0
4
votes
9
replies
399
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
9 hours ago by Gabriel R. ★ 2.9k
1
vote
7
replies
389
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
2 days ago by ntsopoul ▴ 60
6
votes
7
replies
387
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
2
votes
6
replies
384
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
2
votes
8
replies
379
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 5 days ago by 161k • written 5 days ago by ▴ 100
3
votes
3
replies
362
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 3 days ago by ▴ 140 • written 6 days ago by • 0
1
vote
2
replies
359
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 4 days ago by 43k • written 5 days ago by • 0
3
votes
4
replies
353
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 1 day ago by 142k • written 1 day ago by 161k
0
votes
3
replies
353
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
4 days ago by mropri ▴ 150
0
votes
9
replies
347
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
1 day ago by njornet ▴ 20
1
vote
4
replies
345
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 4 days ago by ▴ 30
0
votes
3
replies
344
views
Snakemake wrapper issue
fastqc snakemake
updated 3 days ago by • 0 • written 9 weeks ago by • 0
1
vote
4
replies
340
views
Contig assembly task, errors
dna genetics contig assembly
updated 4 days ago by 43k • written 8 days ago by • 0
0
votes
5
replies
331
views
How to convert normalized BigWig file to count matrix?
count-matrix BigWig
4 days ago by feather-W • 0
0
votes
5
replies
318
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by SilhouetteQ • 0
183 results • Page 1 of 4
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Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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A: Is there a software that can compare phylogenetic trees to each othe (face to fa
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Recent Replies
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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