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122,202 results • Page 671 of 2445
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why hisat2 mapping sam file has many sam flags
sam RNA-seq sequencing hisat2 genome
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Job: Bioinformatics Computer Systems Engineer at Berkeley Lab
systems infrastructure
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 70
4
votes
4
replies
3.6k
views
GATK markduplicates out of memory
Assembly WGS MarkDuplicates GATK
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 540
0
votes
1
reply
1.1k
views
Troubleshooting: rRNA depletion RNAseq no DE genes
R RNA-seq DESEq2 STAR
updated 4.6 years ago by ★ 1.4k • written 4.6 years ago by ▴ 90
1
vote
2
replies
967
views
Does this output indicate my bam is paired end?
samtools
4.6 years ago by curious ▴ 900
0
votes
0
replies
547
views
Individual Gene Association with GWAS SNP data
Limma DE GWAS SNP
4.6 years ago by Harrsha • 0
2
votes
2
replies
1.7k
views
How to analyse a list of GO terms
gene ontology
4.6 years ago by renandosreiss ▴ 10
14
votes
14
replies
4.3k
views
7 follow
Forum: Bioinformatics startup market analysis
startup
written 4.6 years ago by ▴ 30
2
votes
2
replies
6.7k
views
How to count elements with a specific condition in csv file using python
code python csv
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
0
votes
1
reply
788
views
Does PLINK only deal with SNP?
PLINK
updated 4.6 years ago by 11k • written 4.6 years ago by • 0
2
votes
4
replies
1.6k
views
Merge different VCFs from multiple individuals including singletons
VCFTools Genomics
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 30
0
votes
2
replies
978
views
How to normalize 2 samples having 6 separate treatments
normalization
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
3
votes
2
replies
975
views
Phenotrex installation help
microbial phenotrex phenotypes
4.6 years ago by sagrant ▴ 10
0
votes
2
replies
2.9k
views
In KisSplice, I already set "ulimit -s unlimited", but I am still getting stack limit error. Is there a work around this?
snp kissplice rna-seq stack KisSplice
updated 4.3 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
973
views
Job: [Apply by 5/23 ] PhD scholarship on functional and evolutionary genomics
evolution long-read PhD genomics
4.6 years ago by Mari ▴ 30
2
votes
2
replies
3.0k
views
How To Find Data About Tss Of Mirna?
mirna
updated 4.6 years ago by • 0 • written 14.2 years ago by ▴ 10
0
votes
0
replies
978
views
SVA variable of interest in eQTL analysis
sva eqtl
4.6 years ago by Colari19 ▴ 90
1
vote
3
replies
1.5k
views
Overall mappability of genome
gem mappability ngs
4.6 years ago by boczniak767 ▴ 880
2
votes
4
replies
4.0k
views
enrichGO() error: unable to find an inherited method for function ‘keytypes’ for signature ‘"GRanges"’
clusterProfile
4.6 years ago by Trinh ▴ 10
5
votes
5
replies
2.3k
views
Why is there difference FASTA file in an Accession number?
uniprot
updated 4.6 years ago by 154k • written 4.7 years ago by ▴ 10
1
vote
2
replies
1.8k
views
Identify coordinates from the VCF generated from Vg call
call vg vgtool
4.6 years ago by puddingmeow516 ▴ 10
17
votes
21
replies
5.1k
views
8 follow
Forum: bioinformatics thesis
thesis
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 40
0
votes
0
replies
779
views
News: Learn to Analyze and Visualize Microbiome Data with Nephele & MicrobiomeDB
microbiome
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 60
0
votes
0
replies
690
views
How to handle mis-annotated chimeric genes?
chimeric MAKER curation annotation
4.6 years ago by liorglic ★ 1.5k
0
votes
2
replies
1.6k
views
Vg Call, not detecting SV due to soft-clipping
vgteam vg variation graph
4.6 years ago by jcmouren • 0
0
votes
0
replies
1.7k
views
Job: Application data scientist (f/m/d)
Computational-biology
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
0
votes
2
replies
1.1k
views
How to covert Plot_ly codes to ggplot2 codes?
R-studio GWAS visualization ggplot2
4.6 years ago by anikcropscience ▴ 270
0
votes
3
replies
1.8k
views
I tried to compare results which I got it from DESeq2, but got this error?
DeSeq2
4.6 years ago by arulin • 0
2
votes
3
replies
1.2k
views
Coverage required for 3' end RNA-seq methods
cel-seq2
updated 4.6 years ago by 9.0k • written 4.6 years ago by ▴ 390
0
votes
0
replies
666
views
How to Write same Gene name in column with strain identifier!
awk NJ perl Phylogeny
updated 4.6 years ago by 4.2k • written 4.6 years ago by ▴ 30
3
votes
4
replies
2.8k
views
How can I remove ligands in PDB structure?
PDB structure protein
4.6 years ago by jsw940 ▴ 10
1
vote
3
replies
1.9k
views
Tool/method to calculate the sequence context of variants?
sequence context variant
4.6 years ago by Ian 6.1k
0
votes
0
replies
1.7k
views
Midpoint root tree specification.
tree iqtree phylogeny nwk
4.6 years ago by K.Gee ▴ 40
0
votes
0
replies
795
views
Issue with PDB+chain to Pfam mapping and domain filter
Pfam mapping PDB python
4.6 years ago by jmungar2 ▴ 10
2
votes
4
replies
1.2k
views
Indexing
0-based index 1-based
4.6 years ago by GG • 0
0
votes
0
replies
617
views
Whole Metagenome Analysis of resistome dataset
metagenomics ngs
4.6 years ago by hafiz.talhamalik ▴ 350
5
votes
13
replies
4.6k
views
How to calculate percent coverage of each read for nanopore
alignment nanopore sequencing
4.6 years ago by sonsunjirachote • 0
0
votes
0
replies
712
views
How to correct single nucleotide variation due to PCR bias ?
datacorrection rstudio nucleotide merge
4.6 years ago by Gautier • 0
3
votes
2
replies
1.6k
views
Multiple sequence alignment tools
sequence Multiple alignment
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 20
2
votes
2
replies
4.2k
views
Scatter plot of DEG in R
R RNA-seq Bioconductor DEG
4.6 years ago by ATCG ▴ 410
3
votes
0
replies
977
views
How to use IDBA-UD to perform scaffolding on assembled contigs?
IDBA-UD assembly MEGAHIT scaffolds contigs
4.6 years ago by Rui ▴ 50
0
votes
1
reply
971
views
Compare 2 VCF files A & B and return TRUE for every A variant in B, FALSE otherwise
compare vcf
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 40
0
votes
4
replies
1.1k
views
Transcriptome Analysis
RNA-seq Illumina
updated 4.6 years ago by ★ 90k • written 4.6 years ago by • 0
0
votes
0
replies
587
views
ICGC library information
rnaseq
4.6 years ago by camelbbs ▴ 710
0
votes
1
reply
1.1k
views
Using ClueGO without generating a network
Visualization ClueGO
updated 4.6 years ago by ▴ 680 • written 4.6 years ago by • 0
0
votes
2
replies
1.4k
views
Display alignment BAM file
IGV Alignment display RNA-seq
updated 4.6 years ago by ▴ 220 • written 4.6 years ago by • 0
2
votes
1
reply
866
views
Intersecting Wald DESeq2 Results
LRT DESeq2 Wald
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
0
replies
1.5k
views
UK Biobank methylation data
DNA biobank methylation
4.6 years ago by Ivan • 0
6
votes
5
replies
1.8k
views
How to create matrix from row data
sed perl R awk
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 30
0
votes
1
reply
2.5k
views
How to interpret Enrichr combined score 'infinity' value
Enrichr Enrichment
updated 14 months ago by ▴ 100 • written 4.6 years ago by • 0
122,202 results • Page 671 of 2445
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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
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
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Recent Replies
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…
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 …
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