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122,208 results • Page 691 of 2445
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Distance Matrix Calculation
genome biopython
updated 4.7 years ago by ★ 2.2k • written 4.7 years ago by ▴ 140
0
votes
0
replies
817
views
Identification of paralogs having parental/daughter relationship
paralogs
4.7 years ago by arsala521 ▴ 60
2
votes
1
reply
1.8k
views
BWA-MEM or BWA-ALN + BWA-SAMSE for MGI sequencing
bwa ali sequencing
updated 4.7 years ago by 90k • written 4.7 years ago by • 0
3
votes
4
replies
1.7k
views
Alignment Viewer
sequencing alignment
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 40
3
votes
17
replies
4.2k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
4.7 years ago by boczniak767 ▴ 880
0
votes
1
reply
3.4k
views
Regarding valid transcript and Transdecoder output
sequencing Transdecoder transcript assembly
updated 4.7 years ago by ▴ 590 • written 9.6 years ago by ★ 1.9k
0
votes
2
replies
2.9k
views
GAPIT error : invalid '(to - from)/by'
GWAS R programming
4.7 years ago by Inquisitive8995 ▴ 280
3
votes
2
replies
7.6k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
clustering pathways complexheatmap pheatmap
4.7 years ago by Ridha ▴ 130
1
vote
2
replies
1.7k
views
Recommended pipeline for Cut&Run
pipeline
updated 4.1 years ago by • 0 • written 4.7 years ago by ▴ 30
2
votes
3
replies
2.2k
views
BAM file download for just a few genes
RefSeq BAM position RNA-Seq UCSC
updated 4.7 years ago by 14k • written 4.7 years ago by ▴ 110
22
votes
19
replies
8.1k
views
7 follow
FastQTL - GNU Scientific Library (GSL) Domain Error
eQTL GSL RNA-Seq SNP FastQTL
updated 4.7 years ago by • 0 • written 8.8 years ago by ▴ 170
5
votes
4
replies
15k
views
samtools multithreads
samtools
4.7 years ago by Palgrave ▴ 140
2
votes
4
replies
1.9k
views
How to extract the mean quality score of RNAseq for a sample?
FastQC RNAseq Cutadapt illumina galaxy
updated 4.7 years ago by 90k • written 4.7 years ago by • 0
0
votes
7
replies
3.4k
views
Cannot resize rowlabels in aheatmap
clustering aheatmap R
updated 4.7 years ago by 5.8k • written 4.7 years ago by ▴ 20
2
votes
2
replies
2.2k
views
Survival analysis
Cutoff TCGA
updated 4.7 years ago by 5.8k • written 4.7 years ago by ▴ 40
0
votes
4
replies
2.6k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
Pathwayenrichment GeneIdconversion
updated 4.0 years ago by 4.8k • written 4.7 years ago by ▴ 20
0
votes
0
replies
859
views
News: BioSoftics- An Innovative way to explore Science and Technology
genome Biotechnology
updated 4.4 years ago by 45k • written 4.7 years ago by ▴ 10
1
vote
4
replies
2.9k
views
vcftools --TajimaD does not start at 0 and misses variants
vcftools tajimaD
updated 4.6 years ago by 45k • written 4.7 years ago by ▴ 40
0
votes
1
reply
992
views
Missing K-mer in Text
genome alignment
updated 4.7 years ago by 56k • written 4.7 years ago by ▴ 30
2
votes
13
replies
5.6k
views
Get unmapped reads from cram/bam file
alignment
updated 4.7 years ago by 90k • written 4.7 years ago by ▴ 140
4
votes
6
replies
2.3k
views
How can I solve the following error? No module named commons.core.LoggerFactory
python
4.7 years ago by pavelasquezv ▴ 50
2
votes
1
reply
1.7k
views
bedtools getfasta command
fasta
updated 4.7 years ago by ★ 3.9k • written 4.7 years ago by ▴ 40
0
votes
1
reply
960
views
Mendelian vs Inherited variants
inherited mendelian
updated 4.7 years ago by ★ 3.0k • written 4.7 years ago by ▴ 30
2
votes
3
replies
5.7k
views
Converting merged Seurat object back to dgCMatrix
Seurat
4.7 years ago by LacquerHed ▴ 30
5
votes
5
replies
11k
views
Using Seurat to take in a Normalised TPM Gene to Cell matrix as a Seurat Object
format sequencing rna
updated 4.5 years ago by ★ 19k • written 4.7 years ago by • 0
1
vote
2
replies
4.6k
views
Interpreting trim_galore report
RNA-Seq
updated 4.7 years ago by 154k • written 8.3 years ago by ▴ 20
0
votes
1
reply
1.2k
views
2 transcript_id values for the same tRNA in GTF file
GTF arabidopsisthaliana annotation
updated 4.7 years ago by 5.8k • written 4.7 years ago by • 0
2
votes
2
replies
1.2k
views
reformat eland_result.txt to MACS input file
format
updated 4.7 years ago by 103k • written 4.7 years ago by • 0
3
votes
5
replies
5.4k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 4.7 years ago by ▴ 440 • written 7.4 years ago by ▴ 340
0
votes
2
replies
1.4k
views
Analysis of the gene set enrichment in clusters
biopython Fishertest genesetenrichment
4.7 years ago by stgr1202 • 0
0
votes
4
replies
1.8k
views
Puzzling Bowtie2 Input Error -S flag
bash bowtie2 alignment shell
4.7 years ago by geneticatt ▴ 140
0
votes
0
replies
860
views
Job: Postdoc openings @ NYC: Epigenetics / Long Reads / Microbiome
sequencing RNAseq microbiome methylation
4.7 years ago by fanggang ▴ 120
0
votes
0
replies
1.2k
views
Definition of soft threshold power with wgcna: SFT.R.sq vs truncated.R.sq columns
wgcna SFT
updated 2.7 years ago by 45k • written 4.7 years ago by • 0
0
votes
0
replies
430
views
DNAzymes
sequencing
4.7 years ago by maryamtashakori96 • 0
3
votes
4
replies
3.6k
views
Excluding variants with a "LowQual" filter in bcftools consensus
snp bcftools covid-19 ngs
4.7 years ago by cg1440 ▴ 60
7
votes
9
replies
3.9k
views
Choosing a single consensus promoter/transcript for each gene (Mouse)
annotation ucsc general
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 70
1
vote
5
replies
4.8k
views
Issue about "Augustus did not recognize any genes"
Augustus BUSCO
4.7 years ago by boymin2020 ▴ 80
10
votes
10
replies
4.6k
views
7 follow
Pipeline transposable elements
transposon
updated 4.7 years ago by 16k • written 6.5 years ago by ▴ 50
1
vote
1
reply
1.4k
views
Gene sequences for a cell line
genome sequence
updated 4.7 years ago by ▴ 140 • written 4.9 years ago by ▴ 10
0
votes
0
replies
874
views
Stringtie output shows no expression for reference genes
stringtie programming annotation transcriptome rna
4.7 years ago by samhairle ▴ 20
5
votes
1
reply
1.1k
views
How to evaluate phylogenetic congruence between two phylogenetic tree?
snp python perl genomics phylogeny
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 120
8
votes
16
replies
6.2k
views
bedtools bamtofastq generates fastq which cannot be gzip correctly?
gzip miseq bedtools fastq bamtofastq
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 90
3
votes
4
replies
2.5k
views
SARS-Cov-2 variant calling
sequencing variants sars-cov-2
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 130
6
votes
2
replies
5.3k
views
Understanding Seurat Object
RNA-Seq singlecell Seurat
4.7 years ago by patelk26 ▴ 340
1
vote
2
replies
1.3k
views
Is it possible to compare the expression of 2 genes based on count data?
counts RNA-Seq
4.7 years ago by Francois Piumi ▴ 70
14
votes
3
replies
2.6k
views
Is there any gene nomenclature conversion tool that recognizes old names?
genomics R annotation
updated 4.7 years ago by ▴ 340 • written 4.7 years ago by ▴ 70
0
votes
1
reply
1.3k
views
Scoring Metric Gene Clusters (General Inquiry)
genome matrix cluster antismash
updated 4.7 years ago by ▴ 140 • written 5.7 years ago by ▴ 80
4
votes
5
replies
4.1k
views
How to download entire human protein sequences from RefSeq database hrough command line?
Refseq programming
updated 4.7 years ago by ★ 3.9k • written 4.7 years ago by ▴ 80
0
votes
1
reply
875
views
Inclusivity Analysis SARS-CoV2
SARS-CoV-2
updated 22 months ago by 45k • written 4.7 years ago by • 0
3
votes
7
replies
4.4k
views
How to calculate frequencies of SNPs with respect to a particular allele by plink?
frequency snp plink
4.7 years ago by jamespower ▴ 100
122,208 results • Page 691 of 2445
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How to trim transcripts using information from NCBI contamination screen report
How to trim transcripts using information from NCBI contamination screen report
Trimming sequences based on NCBI contamination screen report
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Recent Replies
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!
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…
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