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Recent Replies
Comment: Isoform level TCGA RNA-seq Expression data
by
hofman.bartlomiej
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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…
Comment: Creating sample groups from a combination of genes for survival analysis
by
krushnach80
★
1.1k
**Why not using quantiles? This gives you control over expression range and the ability to determine how wide your high/low label may be.*…
Answer: GATK GenotypeGVCFs explain
by
Zeng Jingyu
▴
40
The official explaination of GenotyeGVCF is [here][1] (4.1.5.0), as the document said it has two types of working mode, for multiple sample…
Comment: Creating sample groups from a combination of genes for survival analysis
by
krushnach80
★
1.1k
Hello @shred I have updated the information regarding your suggestion **Why not using quantiles? This gives you control over expression r…
Comment: ACMG assignment tools
by
Damianos P. Melidis
▴
40
thanks for sharing! Is there a related biorxiv/publication to explain the implementation?
Comment: Creating sample groups from a combination of genes for survival analysis
by
krushnach80
★
1.1k
Sorry for the `you would like to combine the low/high information coming from each gene into a single label to use for a patient` this inf…
Answer: SnpSift to annotate vcf with multiple databases
by
Zeng Jingyu
▴
40
Hi whb, did you try annotate vcf using multiple databases?
I'm now wondering how this could be done.
Comment: Mapping paired end reads with ngm and samtools, using prefixes and suffixes for
by
Human
•
0
hey does this look correct for you ?
#!/bin/bash
(...)
#SBATCH --array=1-262
# Create list of sample names
ls -1 *R1*fastq | xargs …
Comment: My fastq files(paired end) have different read number
by
colindaven
4.5k
Only 2.9% are properly paired. This is bad. You could tell use a bit more about your sequencing project and application and especially ref …
Comment: Creating sample groups from a combination of genes for survival analysis
by
Shred
★
1.0k
It's not clear if you would like to combine the low/high information coming from each gene into a single label to use for a patient. Regard…
Comment: Error when using compareCluster from enichment
by
Basti
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1.4k
Could you show `str(gene_cluster)` ? It is difficult to help without seeing data
Answer: API REST ALINGMENT
by
Shred
★
1.0k
Why reinventing the wheel if they kindly give [code][1] for using their REST API? From https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT…
Answer: Why parametric linkage analysis on Merlin gives zero "0" LOD score?
by
Regina Phalange
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0
Hello! Although it's a very old problem, I have encountered the same issue and it was difficult to find relevant answers through search. Fi…
Comment: Can someone help me with searching overlapping values between two files?
by
mxm189
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0
I tried some stuff but it didnt work. I used ChatGPT, because I'm not good at this.
I tried sorting of the two files first
# Sort the inp…
Comment: Survival analysis with gene expression
by
krushnach80
★
1.1k
Hello @kevinblighe I would like to get your help in [this][1]
[1]: https://www.biostars.org/p/9558148/
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