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122,202 results • Page 682 of 2445
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TMM normalization for data across two sequencing batches
tmm normalization rnaseq
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 40
2
votes
2
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1.5k
views
Why we have exons that start and end at the same coordinate?!
gtf exon GRCh38
updated 4.6 years ago by 48k • written 4.6 years ago by 9.8k
2
votes
3
replies
1.2k
views
Microarray Error
R Microarray
4.6 years ago by rpazo001 ▴ 20
4
votes
7
replies
2.7k
views
Genotype Data in PLINK
Genotype PLINK
updated 4.6 years ago by ★ 4.8k • written 4.6 years ago by • 0
8
votes
2
replies
1.4k
views
How to extract fasta sequences and only its ID's, based on the subsequence fasta numbers from a main fasta file ?
fasta RNA DNA alignment
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 1000
0
votes
0
replies
740
views
Creating a comparison sequence for Multiple sequence alignment in Artemis Comparison Tool (ACT)
multiplesequencealignment artemis
updated 4.6 years ago by 35k • written 4.6 years ago by • 0
0
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0
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1.0k
views
Calculate weighted and unwieghted Unifrac
R MEGA Unifrac
4.6 years ago by chiara.conte91 • 0
0
votes
0
replies
730
views
Error in discretizeDF.supervised(formula, data, method = disc.method) :data needs to be a data.frame
R arulesCBA
4.6 years ago by hebasamysaeid1 • 0
1
vote
3
replies
1.7k
views
Testing independence between 5' and 3' terminal sequences in a DNA database
sequence cluster DNA independence testing
updated 4.6 years ago by 103k • written 4.6 years ago by ▴ 650
1
vote
0
replies
1.5k
views
Job: Bioinformatics Research Analyst - Oncology
oncology genomics
4.4 years ago by Malachi Griffith 20k
7
votes
4
replies
4.7k
views
Visualizing & plotting variant reads within BAM files programmatically?
alignment
4.6 years ago by steve ★ 3.5k
0
votes
0
replies
613
views
Is there any method or algorithm to identify mutation using gene expression information?
algorithm mutation
4.6 years ago by Rida • 0
4
votes
6
replies
2.0k
views
How to extract sub fasta sequences from a multiline fasta file ?
RNA DNA
4.6 years ago by sunnykevin97 ▴ 1000
7
votes
5
replies
8.2k
views
How to convert multiple vcf files to a ped file?
plink vcftools
updated 4.6 years ago by 9.8k • written 9.2 years ago by ▴ 40
0
votes
0
replies
955
views
News: Online training: Data Visualization with Python
Python DataVisualization
4.6 years ago by Physalia-courses ★ 2.7k
2
votes
1
reply
890
views
Phylip/Paml alignment output file explanation ?
RNA alignment DNA
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by ▴ 1000
2
votes
8
replies
2.4k
views
BWA mapping quality 0 for all reads
mapping mapping_quality bwa
updated 4.6 years ago by 103k • written 4.6 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Pathway enrichment with z-scores
Transcriptomics GSEA NGS
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 320
0
votes
0
replies
833
views
Job: Biostatistician Job Opportunity (Bethesda, MD)
Genomics statistics Analysis Rstudio
4.6 years ago by christmasy • 0
1
vote
1
reply
5.2k
views
Removing duplicate varaints in PLINK
plink
updated 4.6 years ago by ▴ 30 • written 4.6 years ago by ▴ 10
1
vote
2
replies
1.3k
views
How to get Python code to run correctly for hetero-dimerization analysis
python sequence programming FASTA
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 320
11
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6
replies
2.3k
views
Forum: Is it still interesting to publish the profile of the transcriptome?
Article RNA Transcriptome Suggestion RNAseq
4.6 years ago by tiagobellintani ▴ 40
1
vote
3
replies
1.5k
views
How to extract de novo transcript from RNA long read alignement ?
RNA pacbio
updated 4.6 years ago by 9.3k • written 4.6 years ago by ★ 2.5k
4
votes
9
replies
9.2k
views
GATK Mutect2 Panel-Of-Normals generation
gatk mutect2 panel-of-normal wes non-tumor
updated 4.6 years ago by • 0 • written 5.4 years ago by ▴ 300
3
votes
4
replies
1.4k
views
How to split the header line into its components
Macspider
updated 4.6 years ago by 21k • written 4.6 years ago by • 0
1
vote
0
replies
853
views
how to tell the OR or BETA in the OR.or.BETA column in GWAS summary statistics from GWAS catalog?
gwassummary gwascatalog
4.6 years ago by zhoufeng2ye ▴ 10
0
votes
3
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1.7k
views
Multiple motif [available in .txt file ] search from large fasta file to find motif frequency then print fasta sequences
motif fasta frequency
4.6 years ago by Swarna Kanchan ▴ 10
2
votes
2
replies
1.4k
views
how to have aligned region in fasta format using blastn?
blastn fasta
updated 4.5 years ago by 45k • written 4.6 years ago by ▴ 80
0
votes
4
replies
2.6k
views
Help with salmon quantification of samples with de novo transcriptome
salmon denovo tximport
updated 4.6 years ago by ▴ 590 • written 4.6 years ago by • 0
2
votes
0
replies
1.0k
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable gatk vcf picard
4.6 years ago by DareDevil ★ 4.5k
0
votes
0
replies
451
views
fetching first column as a class attribute in arulesCBA
arulesCBA R
4.6 years ago by hebasamysaeid1 • 0
1
vote
4
replies
2.3k
views
MA plots with similar distribution but display difference in significantly expressed genes
reads MAplot DEG rna DESeq2
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 10
1
vote
1
reply
1.4k
views
PCA plot making
VCF PCA vcftools SNP
updated 4.6 years ago by ▴ 730 • written 4.6 years ago by • 0
1
vote
0
replies
1.1k
views
Could it be risky to analyse cells that are negative after cell hashing on single cell RNA sequencing?
RNA-Seq singlecell R Seurat
4.6 years ago by charlesgwellem ▴ 10
0
votes
0
replies
1.1k
views
CNVkit flat reference file creation
CNV ces Flatreference CNVkit wes
4.6 years ago by enes ▴ 40
10
votes
4
replies
9.6k
views
What is gnomAD allele frequency
AF gnomAD
updated 22 months ago by ▴ 760 • written 4.6 years ago by ▴ 70
2
votes
3
replies
2.2k
views
Remove reads from bam file that partially covers a region
indel filter bam
4.6 years ago by arbarharw • 0
0
votes
3
replies
1.2k
views
Trim alignment from .sam file based on a specific tab-delimiter .bed file
sam
updated 4.6 years ago by 166k • written 4.6 years ago by • 0
0
votes
0
replies
805
views
SNP Mapping/Characterisation and Patches
GRCh38 prioritisation patches SNP
4.6 years ago by KBMP • 0
0
votes
2
replies
1.3k
views
Help with statistic model
online education R
updated 4.6 years ago by ★ 90k • written 4.6 years ago by • 0
1
vote
2
replies
2.5k
views
Convert multiple rows value retrieved from ensemble biomart to comma separated list for a common ensemble gene ID.
ensembl Biomart R geneontology
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
1.0k
views
UCSC parameters for converting between human genome builds
genomics bed ucsc genotyping
4.6 years ago by jon.klonowski ▴ 210
5
votes
3
replies
1.9k
views
RNA-SEQ count data as input for Machine Learning
machine learning rnaseq normalize
updated 4.6 years ago by ★ 2.9k • written 4.6 years ago by • 0
2
votes
5
replies
2.0k
views
Extracting only tumor samples from Single cell RNASeq
tumor cell singel RNA
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 500
9
votes
6
replies
2.3k
views
6 follow
What are some areas where machine learning is applicable in biology and cancer?
software deep learning
updated 4.6 years ago by ▴ 30 • written 5.9 years ago by • 0
6
votes
11
replies
3.1k
views
How are transcriptome annotations published?
RNAseq annotation publish transcriptome
4.3 years ago by Dunois ★ 2.9k
0
votes
2
replies
1.1k
views
Hetero-dimerization analysis with two FASTA files
sequence FASTA python awk bash
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 320
3
votes
4
replies
2.1k
views
Convert per base bedgraph to Bed format
Bedgraph perbase Bed Bedtools
updated 4.6 years ago by 36k • written 4.6 years ago by ▴ 20
5
votes
4
replies
12k
views
Why is `send` lower than `sstart` from blast format 6 output?
blast genomics
updated 4.6 years ago by • 0 • written 5.8 years ago by ▴ 750
0
votes
0
replies
1.2k
views
bcftools isec not producing sites.txt
bcftools
4.6 years ago by steve ★ 3.5k
122,202 results • Page 682 of 2445
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Comment: low quality data or file name swapping -- cellranger arc errors when processing
Comment: low quality data or file name swapping -- cellranger arc errors when processing
A: Regarding Microarray Platforms
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
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 • 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: 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 • 0
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…
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…
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