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Cell type specificity analysis (microglia+oligodendrocytes)
gene RNA-Seq rna-seq
updated 4.7 years ago by 20 • written 4.8 years ago by • 0
0
votes
2
replies
884
views
Inter-species RNAseq normalisation
EdgeR Deseq2 RNA-Seq Expression Salmon
4.7 years ago by pprice3 • 0
0
votes
1
reply
795
views
to find deleted genes by using python
genome sequencing
4.7 years ago by iqrajaved323 • 0
0
votes
3
replies
975
views
Focusing on a handful of genes during RNA seq
RNA-Seq gene assembly rna-seq
4.7 years ago by snow4964 ▴ 10
0
votes
3
replies
1.6k
views
where can I found ecab3.0 SNP annotation?
snp genome ecab3.0
updated 4.2 years ago by 154k • written 6.0 years ago by ▴ 210
0
votes
0
replies
835
views
Advantages of different methods to transfer GO annotations
RNA-Seq GO Annotation
4.7 years ago by Rogerio Ribeiro ▴ 110
1
vote
2
replies
1.0k
views
CLIP enrichment analysis
ChIP-Seq
updated 4.7 years ago by 22k • written 4.7 years ago by ▴ 80
0
votes
0
replies
611
views
gene info was partially lost while making txdb object from GFF file
RNA-Seq
4.7 years ago by citronxu ▴ 20
0
votes
1
reply
702
views
Mutect2 calls insertion and reverse complement deletion in the same read
alignment sequencing
updated 4.7 years ago by 45k • written 4.7 years ago by • 0
4
votes
3
replies
2.0k
views
Mapping with data stored on external hard disk
alignment rna-seq
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
1
vote
9
replies
4.2k
views
Merge bigwig Files with different intervals
bigwig Merge
4.7 years ago by pt.taklifi ▴ 70
0
votes
2
replies
1.5k
views
Connecting two PDB structures in Pymol
PDB Structures Connect
4.7 years ago by Hansen_869 ▴ 80
0
votes
1
reply
768
views
tool for visualizing small sets of genes
sequence gene
4.7 years ago by goatsrunfaster ▴ 60
2
votes
1
reply
2.9k
views
bedGraphToBigWig error : Expecting at least 3 words line 1 of chrom.sizes. got 2
bigwig bedGraph
updated 4.7 years ago by 90k • written 4.7 years ago by ▴ 70
0
votes
0
replies
948
views
Pymol homology modelling
homology modelling pymol
4.7 years ago by Hansen_869 ▴ 80
1
vote
2
replies
767
views
microRNAs with RNEasy Mini Kit (Qiagen)
RNA-Seq
4.7 years ago by diego1530 ▴ 80
14
votes
10
replies
7.5k
views
bamCoverage bin size for narrow and broad histone marks
ChIP-Seq deeptools
4.7 years ago by Marco Pannone ▴ 810
0
votes
4
replies
965
views
best way to analyze a subset of DE genes
RNA-Seq DESeq expression gene
4.7 years ago by Lila M ★ 1.3k
0
votes
2
replies
1.4k
views
somatic variant calling
variant calling somatic unpaired
updated 4.7 years ago by ▴ 350 • written 4.7 years ago by ▴ 20
1
vote
4
replies
1.9k
views
Processing of shotgun metagenome data
metagenome genome
updated 2.1 years ago by ★ 3.3k • written 4.7 years ago by • 0
2
votes
1
reply
1.3k
views
News: Online Training - Analysis of Transposable elements
genome assembly sequence
updated 7 months ago by ★ 1.3k • written 4.7 years ago by ★ 2.7k
0
votes
2
replies
1.3k
views
Heatmaps for differential expressed probes
R sequencing genome gene
4.7 years ago by gs000095 ▴ 10
0
votes
0
replies
903
views
Using Dgenies from the command line
dgenies alignment
4.7 years ago by langziv ▴ 70
2
votes
5
replies
1.9k
views
Annotating reads with the name of the feature to which they map
RNA-Seq
updated 4.7 years ago by ★ 2.7k • written 4.7 years ago by ▴ 20
0
votes
0
replies
667
views
How to compare two column from two files with specific condition in awk
awk text-processing
updated 4.7 years ago by 21k • written 4.7 years ago by • 0
1
vote
3
replies
2.1k
views
What tools do you use to find the potential off-target sites when designing Cas9/Cas12 RNA-guided endonucleases?
CRISPR off-target alignment
4.7 years ago by genomics0101 ▴ 10
0
votes
4
replies
7.3k
views
Link two proteins in Pymol
pymol link proteins
4.7 years ago by Hansen_869 ▴ 80
0
votes
0
replies
614
views
finding coverage of particular gene sequence from illumina short reads
coverage illumina
4.7 years ago by rthapa ▴ 90
1
vote
2
replies
7.5k
views
Error in reading MatrixMarket file format using Seurat Read10X
RNA-Seq 10x Seurat
updated 4.7 years ago by ★ 8.6k • written 4.8 years ago by ▴ 10
3
votes
3
replies
1.5k
views
probability of observing overlap between sets of genes
R
updated 4.7 years ago by 20 • written 6.3 years ago by ★ 2.6k
1
vote
1
reply
1.1k
views
voomWithDreamWeights() has missing "NA" wheights for last samples
voomWithDreamWeights dream variaincePartition
4.7 years ago by RNAseqer ▴ 300
0
votes
0
replies
1.3k
views
Analyzing RNA-Seq with duplicate ensembl ids using DESeq2: should tximport be used?
RNA-Seq alignment R
4.7 years ago by Ridha ▴ 130
2
votes
4
replies
3.5k
views
F1 Score of Recursive Feature Elimination (RFE) Top 20 features Greater than RFE Cross Validation (CV) F1 Score
sklearn rfe rfecv f1score randomforests
4.7 years ago by ivnnvi • 0
0
votes
0
replies
1.2k
views
How to import a phylogenetic tree (in nexus format) with node support values in R
phylogeny R tree nexus
4.7 years ago by diversitree ▴ 10
2
votes
4
replies
2.0k
views
possible to convert hg19 coordinated position to hg38 coordinated position??
genome snp gene sequencing
updated 4.7 years ago by ★ 4.8k • written 4.7 years ago by ▴ 10
2
votes
0
replies
827
views
Forum: Need recommendations on best certificates to take to boost bioinformatics career and income.
courses
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 20
0
votes
2
replies
918
views
getting fastq ID with SNPs
SNP genome browser fastq
4.7 years ago by bitpir ▴ 250
3
votes
2
replies
954
views
Identifying cancer subtypes
RNA-Seq gene
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 320
0
votes
0
replies
1.2k
views
GATK4 BaseRecalibrator in Galaxy
Galaxy Variant Calling GATK4 BQSR BaseRecalibrator
4.7 years ago by jhy ▴ 10
0
votes
0
replies
822
views
Mapping long RNAseq reads to genome with nextGenMap - how to adjust parameters?
RNA-Seq
4.7 years ago by lechu ▴ 20
2
votes
8
replies
7.5k
views
Heatmap from EdgeR results
edgeR heatmaps DGEList CPM
updated 4.7 years ago by ★ 8.6k • written 4.7 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Hardy-Weinberg equilibrium and GWAS in a livestock species (advice)
HWE GWAS
updated 4.7 years ago by ▴ 900 • written 4.7 years ago by • 0
0
votes
0
replies
949
views
How to visualize sequence annotation results from Trinotate
Trinotate
4.7 years ago by Kash ▴ 110
0
votes
2
replies
1.7k
views
Segmentation fault while running muscle
alignment gene software error
4.7 years ago by alicecol ▴ 20
0
votes
0
replies
1.4k
views
Question about ENCODE ATAC-seq bed file, bed narrowPeak vs bed idr_ranked_peak
ATAC-seq
4.7 years ago by yanweng ▴ 80
4
votes
3
replies
940
views
De novo transcriptome assembly
RNA-Seq
updated 4.7 years ago by ★ 30k • written 4.7 years ago by • 0
3
votes
2
replies
1.2k
views
Expanding gene family using hmmer
hmmer jackhmmer sequence homology
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 80
2
votes
2
replies
2.5k
views
Snakemake (MissingOutputException) doesn't seem to find output files.
Snakemake
4.7 years ago by jkim ▴ 230
0
votes
0
replies
772
views
How do I calculate linkage disequilibrium in 4 mixed ancestry individuals?
SNP genome Linkage disequilibrium Plink
updated 4.7 years ago by 20 • written 4.8 years ago by • 0
1
vote
4
replies
1.2k
views
Group Difference Non-parametric test
R nonparametrictest biostatistics
updated 4.7 years ago by ▴ 10 • written 4.7 years ago by • 0
122,214 results • Page 711 of 2445
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Comment: circos plot for genomic features by colindaven 8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated? by colindaven 8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated? by GenoMax 154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
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 …
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