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189 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 1 hour 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 18 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 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
797
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 23 hours ago by ▴ 90 • written 2.7 years ago by ▴ 80
1
vote
5
replies
795
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
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
641
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
10 hours ago by egascon • 0
1
vote
14
replies
614
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
12 hours ago by hophuquy0944 • 0
0
votes
9
replies
599
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
1 day 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
552
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
4 days ago by Tuck898 • 0
0
votes
1
reply
534
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
2
votes
5
replies
492
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 12 days ago by • 0
5
votes
7
replies
487
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
1
vote
3
replies
433
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
432
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
428
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
4
votes
7
replies
421
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 5 hours ago by ▴ 130 • written 2 days ago by ▴ 20
0
votes
6
replies
420
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
415
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 6 days ago by 142k • written 4 weeks ago by • 0
4
votes
7
replies
411
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
399
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by beginner123 • 0
6
votes
7
replies
387
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
1
vote
7
replies
386
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
2 days ago by ntsopoul ▴ 60
2
votes
6
replies
382
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
4
votes
9
replies
378
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
4 hours ago by Gabriel R. ★ 2.9k
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
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 4 days ago by 43k • written 5 days ago by • 0
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
3 days ago by mropri ▴ 150
3
votes
4
replies
344
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
9
replies
345
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
1 day ago by njornet ▴ 20
1
vote
4
replies
344
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
343
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 3 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
189 results • Page 1 of 4
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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Recent Replies
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.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs by BATMAN • 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
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