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News:
Bioinfo-Core Conference Call, October 17, 2017 (11 am EDT USA, local times around world)
bioinfo-core
updated 21 hours ago by
Ram
38k • written 5.6 years ago by
GenoMax
127k
2
votes
2
replies
2.4k
views
News:
ENCODE 2015: Research Applications and Users Meeting
workshop
mouse-encode
encode
updated 15 hours ago by
Ram
38k • written 7.8 years ago by
Alex Reynolds
34k
6
votes
1
reply
1.7k
views
News:
Are protein domains indivisible?
Athropy
Domains
Proteins
updated 15 hours ago by
Ram
38k • written 7.8 years ago by
Deepak Tanwar
★ 4.2k
4
votes
0
replies
749
views
News:
The BioCompute Object App-a-thon starts on May 14!
standards
computation
pipeline
updated 20 hours ago by
Ram
38k • written 3.9 years ago by
stephens_sarah
▴ 150
2
votes
0
replies
2.2k
views
News:
The NAR annual Web Server Issue is here..
web-servers
updated 20 hours ago by
Ram
38k • written 7.7 years ago by
Antonio R. Franco
★ 5.0k
0
votes
0
replies
950
views
News:
Bioinfo-Core Conference Call, February 6th, 2018 (11 am EST USA and corresponding local times around the world)
bioinformatics-core
bioinfo-core
updated 21 hours ago by
Ram
38k • written 5.1 years ago by
GenoMax
127k
0
votes
0
replies
80
views
News:
course - Reproducibility in Bioinformatics
Bioinformatics
Docker
Reproducibility
18 hours ago by
carlopecoraro2
★ 2.3k
7 results • Page
1 of 1
Recent Votes
RNAseq: same reads + more complete scaffold = fewer DEGs?
Answer: GATK GenotypeGVCFs explain
A: Blast - Formatting Output
A: Blast - Formatting Output
A: Is Paired End analysis possible with FASTQC?
A: How to handle multiple contig outputs from de novo assemblers when one contig is
Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq data
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Pierre Lindenbaum
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Recent Replies
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
by
GenoMax
127k
> So, I prefer to work assembled fastq files into one fastq rather than > two. What does this mean? Are you concatenating two sets of file…
Comment: What is exactly meant by "GENCODE TSS"?
by
ntsopoul
▴ 40
checkout: chipseeker package there is a function which gets you the tss getPromoters(TxDb=txdb, upstream=3000, downstream=3000) as you c…
Comment: SRA Taxonomy Analysis - difference between tables and web
by
GenoMax
127k
> Apparently it is ok for some accessions In that case, your best bet is to contact NCBI help desk with examples of what works and what do…
Comment: how to calcul risk score with a prognostic genes
by
Sarah
▴ 30
I did it manually. you multiply your gene expression by the coxPH coefficient.
Comment: Circos plot using vcf : Mutect2 MultiSample VCF out file
by
m. bioinfo
• 0
thanks Pierre ! and I suspect this .bed output should be used as input for Circos. Do I need any corrections here ? 😊
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs?
by
Darked89
4.2k
Assuming that the genes are spliced and that new assembly => new annotation. One possibility is that previously counted as 2 or more gene f…
Comment: How to include spatial coordinate data into anndata within scanpy
by
Omics data mining
▴ 210
I am still struggling with this. I tried to add data manually, it gives me error. Would you please give me example to add spatial into h5a…
Comment: prefix extraction and preparation for mapping and variant calling
by
Joe
20k
You are explicitly specifying the suffixes in your commands, so it's entirely up to you if you stick to this, or you wish to define them ea…
Answer: GATK GenotypeGVCFs explain
by
Sarah
▴ 30
thank you all !
Comment: OrthoFinder problem
by
HERMAN
▴ 10
Hi Mike, It does not produce any error message, the software just freezes. I let it run for 1h without any improvement. I have come with…
Comment: What is exactly meant by "GENCODE TSS"?
by
Pierre Lindenbaum
153k
> How do you differentiate the case where for an alternate transcript of gene A, the first exon is NOT the first transcribed exon (due to s…
Comment: OrthoFinder problem
by
shelkmike
▴ 920
What error message does OrthoFinder produce?
Answer: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da
by
benformatics
3.5k
I would go with SUPPA2 or rMATS. You can see some benchmarking here: https://www.nature.com/articles/s41467-023-36585-y
Comment: CluserProfiler message "No gene can be mapped"
by
joe555
• 0
You were right. The author kindly replied and I also found this: https://github.com/YuLab-SMU/clusterProfiler/issues/561 The latest github…
Comment: Isoform level TCGA RNA-seq Expression data
by
hofman.bartlomiej
• 0
If I may ask, how did you obtain Isoform level RNA-seq data from TCGA? I am trying to do so via TCGAbiolinks R package, however, without po…
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