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122,200 results • Page 624 of 2444
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4
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1.8k
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Lexogen Quantseq Mapping Rates with Salmon
Quantseq RNAseq Salmon Lexogen Mapping
4.3 years ago by abnerapsley • 0
0
votes
0
replies
660
views
Increase in discordant alignments with Bowtie2 after changing trimming stringency?
cutadapt trimgalore ATAC-seq stringency bowtie2
4.4 years ago by uli • 0
1
vote
2
replies
2.0k
views
small RNA-Seq analysis and doubts
nc RNA-Seq small miRNA-Seq
4.4 years ago by Sergio • 0
2
votes
2
replies
1.4k
views
merging paired ends illumina reads without quality with Pear
pear merging illuminareads
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
0
votes
1
reply
808
views
How to get all the metabolic pathways present within a bacteria species?
database
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 250
0
votes
0
replies
808
views
News: Online training - Introduction to Deep Learning in biology
DeepLearning
4.4 years ago by Physalia-courses ★ 2.7k
5
votes
2
replies
7.7k
views
TPM to log2(TPM+1)
log TCGA KIRC RNA-seq TPM
4.4 years ago by David ▴ 30
1
vote
1
reply
1.7k
views
Downloading the RefSeq proteins complete data set
ftp refseq
updated 4.4 years ago by 154k • written 4.4 years ago by ★ 2.9k
2
votes
2
replies
2.5k
views
How to write the rule for Indexing with bowtie2-build and Expand function in snakemake ?
bowtie2 snakemake indexing
updated 4.4 years ago by 90k • written 4.5 years ago by • 0
0
votes
0
replies
573
views
Autodock4
Autodock4
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
0
votes
6
replies
2.1k
views
tool to identify genomic structural variations in completely sequenced prokaryotic genomes
prokaryotes genomic variations mugsy structural
updated 4.4 years ago by ▴ 640 • written 4.4 years ago by • 0
0
votes
2
replies
2.3k
views
Imputation of X chromosome non-PAR for male subjects
SNP imputation X chromsoome
4.3 years ago by Apprentice ▴ 190
0
votes
1
reply
1.1k
views
defining input files for SeqIO
SeqIO python
updated 4.4 years ago by ▴ 650 • written 4.4 years ago by • 0
3
votes
1
reply
849
views
Annotating an assembly according to alignment against a reference genome
genbank annotation alignment
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 70
0
votes
1
reply
892
views
Degenerate Primer Sequence Recovery
python degenerate-primers
updated 2.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
1
reply
3.7k
views
BL21 vs BL21 Star
E.coli BL21
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 180
0
votes
0
replies
817
views
snpeff effect prediction confusion
variant hgvs snpeff annotation
4.4 years ago by najoshi ▴ 30
0
votes
2
replies
1.0k
views
Chip seq data related query
values Chip data narrowPeak intensity
4.4 years ago by sujasubramanian ▴ 70
0
votes
4
replies
2.0k
views
Issues with genome indexing with bowtie2-build
bowtie2 index
updated 4.4 years ago by 5.3k • written 4.4 years ago by • 0
9
votes
13
replies
6.0k
views
error when running bbduk
bbduk
updated 17 months ago by 45k • written 4.4 years ago by ★ 1.3k
9
votes
6
replies
4.1k
views
Trouble running snakemake while defining maximum RAM usage
snakemake
updated 4.4 years ago by 15k • written 4.4 years ago by ★ 1.2k
0
votes
0
replies
683
views
KEGG pathway analysis of miRNA in rice(oryza sativa)
target kegg pathway miRNA prediction
4.4 years ago by Aswini • 0
1
vote
3
replies
1.6k
views
CURL UniprotIDs not working consistently
curl uniprot python bash
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
0
votes
0
replies
670
views
How to divide reads mapping to two different genes using featureCounts
featureCounts mapping alignment rna-seq
4.4 years ago by Apex92 ▴ 320
12
votes
10
replies
2.5k
views
Ensure identical output between platforms and operating systems
reproducibility
updated 4.4 years ago by 36k • written 4.4 years ago by 90k
9
votes
9
replies
11k
views
I couldn't install DEseq2?
R rna-seq gene
updated 4.4 years ago by 90k • written 6.6 years ago by ▴ 20
3
votes
2
replies
1.2k
views
Help needed in retrieving data from Candida genome database
candida R
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Source incompatible with Sink
CWL
4.4 years ago by Levi ▴ 10
1
vote
2
replies
1.5k
views
pyscenic
pyscenic
4.4 years ago by Wakala • 0
7
votes
2
replies
7.2k
views
Trinity : How To Co-Assemble Different Samples (Tumor And Healthy)
trinity assembly transcriptome
updated 4.4 years ago by ▴ 20 • written 13.8 years ago by 11k
2
votes
5
replies
6.9k
views
Adding Introns To Gff3 Format?
coordinates gff3 conversion
updated 4.4 years ago by 45k • written 12.8 years ago by ▴ 960
3
votes
4
replies
2.3k
views
sugestion nanopore assembly and illumina reads
nanopore assembly illumina
updated 4.4 years ago by ★ 2.1k • written 4.4 years ago by ▴ 70
4
votes
8
replies
2.7k
views
Aligning two fasta files with multiple sequences
Protein Fasta Sequence Alignment
4.4 years ago by Ammar Danazumi ▴ 10
0
votes
2
replies
738
views
Clustering based on sequence similarity
relativenessbasedclustering
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
1
vote
7
replies
4.3k
views
Error when running hhblits: Cannot allocate memory/Could not read index file...
software error hhsuite hhblits
updated 4.4 years ago by ★ 2.9k • written 5.9 years ago by • 0
0
votes
0
replies
863
views
SKAT-O R Error
SKAT R
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
4
votes
5
replies
1.4k
views
Efficient ways to retrieve all sequences associated with a disease?
Sequences data-mining monogenetic-disorders
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 10
3
votes
10
replies
3.9k
views
VEP is returning ClinVar fileds bank (-- custom annotation with VEP)
ClinVar VEP annotation
updated 4.4 years ago by 24k • written 4.4 years ago by • 0
0
votes
2
replies
2.2k
views
Integrate CITESeq reads to Seurat object
scRNAseq CITEseqCount Seurat CITEseq
updated 4.4 years ago by ▴ 20 • written 4.4 years ago by • 0
6
votes
2
replies
10.0k
views
Tools to generate spliced/unspliced counts
velocyto single-cell splicing RNA-seq scvelo
4.4 years ago by PianoEntropy ▴ 70
2
votes
3
replies
1.4k
views
shell command to the following question
linux offtopic
updated 4.4 years ago by ★ 2.9k • written 4.4 years ago by ▴ 70
3
votes
1
reply
3.6k
views
Normalization and Batch Effect of bulk RNA-Seq
batch RNA-Seq correction normalization
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 200
2
votes
2
replies
1.7k
views
Genome aligner that shows annotations too
alignment genome annotations
4.4 years ago by danvoronov ▴ 30
1
vote
3
replies
2.2k
views
Species level taxID
blast taxIDs edirect ncbi
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 30
1
vote
2
replies
1.5k
views
Samtools pileup extract read length for position
SNP pileup samtools bam
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 30
2
votes
4
replies
1.8k
views
[SOLVED] GSEA - Strange Results interpretation - Error in DESEQ2 ?
gsea deseq2 clusterprofiler
4.4 years ago by Evan ▴ 250
0
votes
0
replies
860
views
Change axis of ProDy plot
python python3 ProDy matplotlib
4.4 years ago by Kevin ▴ 70
1
vote
5
replies
2.4k
views
Unusual FastQC Per Base Sequence Content
FastQC Illumina
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 10
20
votes
12
replies
42k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
perl python awk
updated 2.7 years ago by 45k • written 11.9 years ago by 9.8k
3
votes
4
replies
1.8k
views
how to detect non CpG methylation probes ?
DNAmethylation methylation infinium450k microarray minfi R
4.4 years ago by takoyaki ▴ 120
122,200 results • Page 624 of 2444
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Answer: best practice for diploid variant calling
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
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Recent Replies
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk • 0
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 • 0
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!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
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