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0
votes
2
replies
1.6k
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Lengths of UTR3, UTR5 and ORF from gtf file
UTR ORF
4.7 years ago by bio_elle ▴ 10
0
votes
4
replies
1.6k
views
Plotting PCA and Admixture for CNVs
R
updated 4.7 years ago by 45k • written 4.7 years ago by • 0
2
votes
4
replies
1.9k
views
How to download viral subset of the UniProt Reference Clusters?
swissprot database uniprot
updated 4.6 years ago by ★ 2.4k • written 4.7 years ago by ▴ 60
0
votes
1
reply
2.4k
views
Dispersion and variance in RNA-seq explained.
RNA-Seq
updated 3.7 years ago by 45k • written 4.7 years ago by ▴ 140
0
votes
0
replies
1.2k
views
How do I solve "incompatible numba" while installing Scanpy?
RNA-Seq alignment
4.7 years ago by Olalekan • 0
0
votes
3
replies
2.6k
views
antismash 5.0 (New region concept) - counting BGCs
antismash metagenomics
updated 4.7 years ago by ▴ 140 • written 5.2 years ago by ▴ 110
0
votes
0
replies
1.2k
views
merge DRAGEN vcf
structuralvariants DRAGEN mergevcf
updated 4.7 years ago by 14k • written 4.7 years ago by • 0
0
votes
0
replies
1.1k
views
How to interpret output of SAM/SAMseq in R (samr package)
R
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 110
0
votes
0
replies
1.1k
views
SAM: why NM and MD tag are changed by the picard tool SetNmMdandUqtag ?
alignment gatk sam
4.7 years ago by quentin54520 ▴ 120
0
votes
3
replies
869
views
emboss skipredundant issue
alignment sequence
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
0
replies
807
views
ENSEMBL bigwig RNA-seq tracks for single-gene visual inspection
RNA-Seq tracks bigwig ensembl zebrafish
4.7 years ago by bernarda • 0
0
votes
2
replies
1.3k
views
Which Bioinformatic tools are used for NRPS Domain analysis?
NRPS NRPS analysis Domain prediction
updated 4.7 years ago by ▴ 140 • written 6.7 years ago by • 0
9
votes
3
replies
1.7k
views
Should I contact an author if I can (or cannot) find their data ?
reads dataset publication
updated 4.7 years ago by 56k • written 4.7 years ago by ▴ 20
1
vote
2
replies
1.6k
views
Does Jellyfish k-mer counting tool give wrong k-mers?
software error
4.7 years ago by rubyeat88 ▴ 10
1
vote
2
replies
974
views
Want to know whether this p-adj value is acceptable
RNA-Seq next-gen sequencing
updated 4.7 years ago by 90k • written 4.7 years ago by ▴ 10
50
votes
20
replies
8.6k
views
18 follow
Forum: Explain bioinformatics to a 10 year old
bioinformatics
updated 2.7 years ago by 45k • written 9.7 years ago by ★ 1.1k
0
votes
0
replies
650
views
Gene Ontology with Locus referring
GO gene
4.7 years ago by rrapopor ▴ 40
0
votes
0
replies
734
views
Plotting PCA and Admixture for CNVs
genome
4.7 years ago by hosin • 0
0
votes
2
replies
1.2k
views
Discrepancy between Genome Browser hg19 phyloP Score and that of wig data
phyloP genome browser
4.7 years ago by progistar ▴ 40
2
votes
2
replies
5.1k
views
Whole Blood Gene Expression Deconvolution
expression
updated 4.7 years ago by 20 • written 11.6 years ago by ▴ 90
1
vote
5
replies
2.4k
views
chi squared assesment of gene expression and batch effect
RNA-Seq r chi squared
4.7 years ago by RNAseqer ▴ 300
0
votes
1
reply
1.5k
views
model matrix error message 'unequal columns/rows' when using a conditional variable
rna-seq categorical variables edger
updated 4.7 years ago by ★ 8.6k • written 4.7 years ago by ▴ 300
0
votes
5
replies
2.1k
views
I am scaffolding using HiC data and found many contigs are out of the chromosome. Please help me.
sequencing assembly
updated 4.7 years ago by 56k • written 4.7 years ago by • 0
4
votes
3
replies
1.5k
views
Vertically merge dataframes in R from a list
R
4.7 years ago by ellieuk ▴ 40
0
votes
2
replies
1.2k
views
How to make paired-end sequencing multi-mapping reads have only the optimal two reads
RNA-Seq alignment sequencing
4.7 years ago by minghuiguo448 • 0
0
votes
1
reply
1.0k
views
Deletions together with SNVs on BAM files
alignment sequencing genome browser
4.7 years ago by baliczap • 0
2
votes
0
replies
910
views
3D distance between two chromosomal coordinates in 3D human genome?
3d hi-C genome chia-pet
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 20
0
votes
0
replies
829
views
copy number of gene in the gap of segmentation file
WES copy number sequenza
4.7 years ago by xiaoqiaoliu • 0
0
votes
1
reply
938
views
Nesting a covariate for differential expression design
RNA-Seq nested covariates
updated 4.7 years ago by 20 • written 4.7 years ago by ▴ 300
2
votes
2
replies
2.0k
views
Why PLINK is producing different LD result with the same dataset?
SNP sequence genome R software error
updated 4.7 years ago by ★ 4.8k • written 4.7 years ago by ▴ 270
0
votes
2
replies
2.9k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
kegg database metagenomics module
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 750
1
vote
5
replies
3.5k
views
Soft-clipping of a BAM file based on regions from the BED file
rna-seq
updated 4.6 years ago by 166k • written 4.7 years ago by ▴ 20
3
votes
2
replies
2.0k
views
Forum: If I want to learn bioinformatics as a computer scientist, would it help to learn Data science and Machine Learning first?
computer-scientist machine-learning
updated 2.7 years ago by 45k • written 4.7 years ago by • 0
0
votes
2
replies
1.6k
views
Lmfit function, to analyse differential expressions, not coming from arrays
gene
updated 4.7 years ago by 105k • written 4.7 years ago by • 0
0
votes
6
replies
3.2k
views
IDT xGen Exome Research Panel v2 vs Twist Human exome core
next-gen genome sequence
updated 4.7 years ago by ★ 3.0k • written 4.7 years ago by ▴ 20
2
votes
1
reply
979
views
How do I make my code go through all through my list in my file.
sequence
updated 4.7 years ago by 11k • written 4.7 years ago by • 0
1
vote
1
reply
2.5k
views
Download pfam sequence
sequence
updated 4.7 years ago by 20 • written 5.6 years ago by ▴ 140
0
votes
1
reply
1.3k
views
Cheat Sheet for NGS data analysis
next-gen cheat-sheet guidebook pdf NGS
4.7 years ago by angsudas62 • 0
3
votes
5
replies
1.9k
views
Forum: Hide Emails from Guests
meta biostars
updated 2.7 years ago by 45k • written 5.0 years ago by ▴ 840
7
votes
9
replies
1.5k
views
6 follow
Bioinformatics research work
genome snp assembly
updated 4.7 years ago by 56k • written 4.7 years ago by • 0
0
votes
1
reply
1.8k
views
Is there any software/tool that can be used to identify/count the number of feed forward loops and feedback loops in the gene regulatory networks?
Biological Networks Systems Biology
updated 4.7 years ago by 20 • written 8.3 years ago by • 0
0
votes
0
replies
579
views
STRING databases in exome sequencing
genome
4.7 years ago by storm1907 ▴ 30
0
votes
3
replies
1.0k
views
Problem installing bioconductor package 'sesameData' (R 4.0, Bioc 3.12)
R bioconductor sesameData sesame TCGAbiolinks
4.7 years ago by mario.red8976 ▴ 140
5
votes
2
replies
1.9k
views
Question about the sped of the global pairwise alignment of Bio.pairwise.align.globalms and Align.PairwiseAligner()
Python pairwise global aignment
4.7 years ago by master_zhen ▴ 10
0
votes
1
reply
844
views
How to normalise read depth in scRNA-seq data, with usegalaxy
scRNA-seq read-depth
4.7 years ago by ikokkinopoulos • 0
1
vote
3
replies
25k
views
Converting .txt into .fasta
sequence
updated 4.7 years ago by ▴ 20 • written 4.7 years ago by • 0
4
votes
4
replies
2.1k
views
Gene ID problems when mapping and counting
RNA-Seq
4.7 years ago by hellocita ▴ 40
0
votes
0
replies
852
views
Looking to annotate concatenated VCF files on Galaxy for Hg19 reference genome. Need setup guidance.
genome next-gen sequencing sequence gene
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Post Alignment basic QC of RNA-Seq data
alignment RNA-Seq
updated 4.7 years ago by 15k • written 4.7 years ago by ▴ 80
0
votes
0
replies
1.4k
views
mummerplot - providing ranges for x and y axes
mummer nucmer mummerplot
updated 4.7 years ago by 45k • written 4.8 years ago by ▴ 70
122,211 results • Page 696 of 2445
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Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 130
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
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