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122,202 results • Page 689 of 2445
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HaplotypeCallerSpark
Variant gatk haplotypecaller
updated 3.7 years ago by • 0 • written 4.7 years ago by ▴ 120
2
votes
5
replies
3.3k
views
What is the most accurate short (ish) read aligner?
aligner sequencing bwa minimap2
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 120
0
votes
1
reply
1.1k
views
MSI cslculation
bed sequencing annotation
updated 4.7 years ago by ★ 3.0k • written 4.7 years ago by • 0
0
votes
0
replies
1.0k
views
How to covert VCF-like to ICGC-like vcf Format
conversion annotation
4.7 years ago by Alewa ▴ 190
6
votes
5
replies
3.9k
views
Comparison of samples to find the best parameters for RNA-seq
NGS rna fastq R sequencing
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 30
0
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1
reply
837
views
Problem featurecounts 0 assigned with canfam4, only less than 20% with canfam3 dog genome
rna-seq
updated 4.7 years ago by 103k • written 4.7 years ago by • 0
8
votes
14
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4.1k
views
6 follow
Another infer_experiment.py interpretation question
RNA-Seq sequencing
updated 3.0 years ago by 154k • written 4.9 years ago by ▴ 20
0
votes
2
replies
1.2k
views
IF statement (in linux script) to merge Fastq files with similar (but not the same) names
unix script ifstatement linux fastq
updated 4.7 years ago by 21k • written 4.7 years ago by ▴ 40
2
votes
3
replies
2.0k
views
Add Strand tag to hisat2 alignments
rna hisat2
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 400
4
votes
4
replies
8.4k
views
Transcriptome assembly -- fastp vs Trimmomatic
trimming transcriptome
updated 16 months ago by ▴ 40 • written 4.7 years ago by ▴ 290
0
votes
1
reply
3.3k
views
How are SNP distance matrices made?
matrix SNP distance CFSAN pipeline
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 30
1
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2
replies
4.0k
views
Snakemake how to use glob_wilcards properly
glob wildcards snakemake python
4.7 years ago by Peter Chung ▴ 210
0
votes
3
replies
1.9k
views
RSEM Calculate Expression Error
rsem frequency coding RSEM sequencing
updated 4.5 years ago by ▴ 70 • written 4.7 years ago by • 0
1
vote
2
replies
1.5k
views
Why I get three file by makeblastdb?
blast
4.6 years ago by 153348734 • 0
10
votes
3
replies
4.0k
views
Blast hits output to fasta format ?
alignment assembly blast
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 1000
1
vote
5
replies
2.0k
views
DeSeq2 analysis - very low variability among replicates
edgeR deseq2 rnaseq
updated 4.7 years ago by 90k • written 4.7 years ago by ▴ 70
0
votes
0
replies
736
views
Charmm force field for octanoic acid
Charmm Gromacs Stimulation
updated 4.7 years ago by 90k • written 4.7 years ago by • 0
1
vote
0
replies
644
views
Does GATK4 provide better quality of SNP/Indels calls over GATK3.8?
sequencing
updated 4.7 years ago by ★ 90k • written 4.7 years ago by ▴ 10
0
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4
replies
5.2k
views
featureCount not processing reads
featureCounts RNA-Seq Rsubread
updated 4.2 years ago by 45k • written 11.0 years ago by ▴ 100
0
votes
1
reply
1.3k
views
How to create a dummy GFF file from fasta?
fasta coverage bed gff
4.7 years ago by O.rka ▴ 750
2
votes
2
replies
2.2k
views
is quality evaluation of transcriptome assembly still required if my workflow is (good quality reads (fastp) -> bowtie2 alignment to reference genome…
RNA-seq transcriptome
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 180
1
vote
2
replies
3.0k
views
single cell sequencing data doublets removal tools selection
sequencing
updated 4.7 years ago by ★ 2.1k • written 6.5 years ago by ▴ 350
7
votes
4
replies
2.1k
views
SARS-CoV2 strain identifying strain
Covid19 SARS-CoV-2 GISAid
updated 22 months ago by 45k • written 4.7 years ago by ▴ 100
0
votes
0
replies
1.3k
views
alternative package for littlesMCAR() or mcar_test()
littlesMCAR MCAR missingdata
4.7 years ago by RNAseqer ▴ 300
0
votes
0
replies
878
views
Job: Postdoctoral fellowship in Bioinformatics in Houston
RNAbiology python sequencing
updated 4.4 years ago by 45k • written 4.7 years ago by • 0
14
votes
10
replies
3.7k
views
6 follow
How to reverse the order of **records** in a fasta file
sequence pipeline programming fasta
updated 4.6 years ago by 21k • written 4.7 years ago by ▴ 320
1
vote
4
replies
5.3k
views
[E::bwa_idx_load_from_disk] fail to locate the index files
bwa
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Identification of protein domain encoding multi-exon genomic intervals
geneprediction
4.6 years ago by Anand Rao ▴ 650
2
votes
2
replies
1.2k
views
Adding mean and error onto scatterplot data
rstudio rna-seq ggplot
4.7 years ago by julianneradford ▴ 20
1
vote
4
replies
1.8k
views
ChIPQC reporting fewer reads in bam than are actually present
R ChIPseq ChIPQC
4.7 years ago by gkunz ▴ 30
0
votes
1
reply
1.1k
views
Observation weights in zinbwave and it's use in deseq
zinbwave data deseq
updated 4.7 years ago by ★ 90k • written 4.7 years ago by • 0
2
votes
1
reply
1.1k
views
Converting Aminoacid MSA alignment to Nucleotide MSA alignment ?
nucleotide dna alignment protein rna
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 1000
0
votes
0
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1.5k
views
Job: Fully Funded Multiple PhD Positions in the interface of Machine Learning(Deep Learning) and Health Informatics (including Bioinformatics and Clinical…
deeplearning analytics python
updated 4.4 years ago by 45k • written 4.7 years ago by • 0
0
votes
2
replies
1.4k
views
Tabix file format
MatrixeQTL Tabix miRNA
4.7 years ago by georgians ▴ 50
0
votes
0
replies
818
views
Generating plots from lima report: demultiplex pacbio .bam files
demultiplex Barcode PacBio
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
1
reply
1.8k
views
Determine the significance of peak overlaps (bedtools)
bedtools peak ChIP-seq eCLIP
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 110
0
votes
1
reply
1.1k
views
Batch effect correction without detecting any clustering on batches
batch-effect rna RNA-seq
4.7 years ago by SHN ▴ 40
2
votes
4
replies
3.8k
views
Which formula of Bray-Curtis beta diversity index should be used for microbiome beta diversity analysis?
diversity
updated 4.7 years ago by 3.4k • written 4.7 years ago by ▴ 250
0
votes
0
replies
862
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
ppi cancer networks genomics
4.7 years ago by martin.schaefer ▴ 10
0
votes
1
reply
1.1k
views
Integrating mRNA expression data with chips data to get the epigenetic profiles of H3k27me3, H3K4me3 and EZH2 in GBM
pipeline
updated 4.7 years ago by ★ 19k • written 4.7 years ago by ▴ 30
4
votes
4
replies
1.6k
views
Will mapping Read 1 in Single Cell 3' sequencing increase mapping accuracy or not?
singlecell zUMI mapping 3`sequencing scruff
updated 4.7 years ago by 154k • written 4.7 years ago by ★ 2.2k
5
votes
2
replies
2.5k
views
Infering strand specificity of bam files using rseqc?
RSeQC bam featureCounts
updated 4.7 years ago by 103k • written 4.7 years ago by ★ 4.5k
5
votes
4
replies
1.7k
views
Bowtie2 unpaired mode usage
sam bowtie2
4.7 years ago by Jimpix ▴ 10
0
votes
3
replies
1.4k
views
RNA seq data analysis without control samples
novelandtranscriptisoforms RNAseq
4.7 years ago by vasanthmandla • 0
5
votes
7
replies
19k
views
How to identify cell types using addModuleScore function?
single cell RNA-seq
updated 4.4 years ago by ▴ 120 • written 5.2 years ago by ▴ 190
1
vote
4
replies
2.9k
views
BLAST results shows partial matches
blast BLAST assembly
4.7 years ago by langziv ▴ 70
10
votes
18
replies
4.9k
views
How to concatenate FASTA files in a specific order based on sequence ID
sequence fasta awk python pipeline
4.7 years ago by Apex92 ▴ 320
5
votes
4
replies
1.5k
views
Could I analyze just a few genes of a BAM file?
RNA-Seq BAM
updated 4.5 years ago by 45k • written 4.7 years ago by ▴ 110
1
vote
2
replies
1.4k
views
Some questions about the CPTAC data processing
programming genomics protein
4.6 years ago by tujuchuanli ▴ 140
1
vote
1
reply
1.1k
views
Forum: Sharing frequently asked questions about microbial genome sequencing II
microbial faq genome sequencing meta
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 520
122,202 results • Page 689 of 2445
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what cause poly-G from NextSeq
what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
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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