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News:
Training in Variant Analysis @NIH, USA, April 16-19,2019
genotype
phenotype
updated 22 hours ago by
Ram
38k • written 4.1 years ago by
AABI
▴ 130
0
votes
0
replies
455
views
News:
Training in Variant Analysis @NIH, January 28-31, 2020
Variant-Calling
next-gen
genome
updated 20 hours ago by
Ram
38k • written 3.3 years ago by
AABI
▴ 130
0
votes
0
replies
98
views
News:
ISMB-affiliated virtual tutorial on Neo4j/Cypher for life sciences
neo4j
cypher
graph
knowledge
19 hours ago by
Stephen
• 0
0
votes
0
replies
98
views
News:
course - Reproducibility in Bioinformatics
Docker
Reproducibility
updated 18 hours ago by
Ram
38k • written 2 days ago by
carlopecoraro2
★ 2.3k
0
votes
0
replies
91
views
News:
Announcing workshop on Declarative Programming in Biology and Medicine (Seattle, Sept. 2023)
medicine
declmed
declarative
icfp
precision
21 hours ago by
Stephen
• 0
0
votes
0
replies
18
views
News:
NCBI's IgBLAST version 1.21.0 is now available
IgBLAST
BLAST
T-Cell
NCBI
receptors
updated 56 minutes ago by
GenoMax
127k • written 1 hour ago by
PeterC_NCBI
▴ 200
6 results • Page
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Recent Votes
A: What Makes One Probability Distribution Better For Rna-Seq Than Another?
Answer: How to demultiplex single end - dual index run - NextSeq 500
How to calculate Exon-Intron junction perbase coverage?
Comment: how to get to a VCF from bam files
Answer: Snakemake error to build synteny from BUSCO .tsv
How to find promoter sequence of a gene?
Answer: How to demultiplex single end - dual index run - NextSeq 500
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Recent Replies
Comment: SKAT in R
by
Pierre Lindenbaum
153k
cross-posted: https://bioinformatics.stackexchange.com/questions/20772
Comment: Samtools fixmate: whta's wrong with the terminal?
by
Pierre Lindenbaum
153k
oh , Ram was too fast ! :-D
Answer: Samtools fixmate: whta's wrong with the terminal?
by
Pierre Lindenbaum
153k
1) your [standard][1] output is redirected to the terminal instead of a [file][2]. 2) there is no such option `-0` (zero) . your want …
Answer: multiallelic variants
by
raphael.B
▴ 290
you can use bcftools norm on your vcf to split multiallelic records prior to merging
Answer: Samtools fixmate: whta's wrong with the terminal?
by
Ram
38k
The output format parameter is `-O`, not `-0`. Also, there's a `-` before the `path/` which makes samtools thing `ath/file_fixmated.bam` is…
Comment: lncTar
by
Ram
38k
> Zea maize Is that a typo or a pun on *Zea mays* being maize?
Comment: How to demultiplex single end - dual index run - NextSeq 500
by
Apex92
▴ 260
Thank you for your input it was helpful.
Comment: normalized score for SpatialFeaturePlot
by
jv
★ 1.0k
not sure that this is the issue, but are you sure that `SpatialFeaturePlot` is pulling from the SCT assay in each case? Another way to ask …
Comment: Python formatting when visualizing Primer3-py dimers
by
Wayne
★ 1.6k
You should include all your code to produce your toy example so that others can pick up with what you have worked. And then more likely you…
Answer: LncTar error !!!
by
Amrendra
• 0
I found lncRNA from transcriptome data. Now, I'm trying to identify the target from the mRNA of Zea maize with the help of LncTar tools, bu…
Comment: How to demultiplex single end - dual index run - NextSeq 500
by
GenoMax
127k
You must know that this flowcelll was run as say 50x8x8x50. Length of the index cycles here 8 matches your indexes in the samplesheet. You …
Comment: how to get to a VCF from bam files
by
Ram
38k
The approach works, yes, but you're no longer calling per-sample variants. `*.bam` is dangerous for a beginner - the chances of something g…
Comment: NCBI's Foreign Contamination Screen (FCS) tool improves the quality of GenBank
by
PeterC_NCBI
▴ 200
Thank you for the feedback. I'll pass it along to the team. Yes, it does require a lot or RAM. One option of course would be to run it on t…
Answer: How to find promoter sequence of a gene?
by
Getting there
▴ 90
I would start with ENCODE data here [ENCODE PROJECT][1] You can select a specific transcription factor you are interested in, a tissue t…
Comment: SKAT in R
by
acvill
▴ 290
I have no sense of whether SKAT is the right tool for your analysis, but some insight into your errors: did you mean `data = snps` instead …
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