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Recent Replies
Comment: Getting species names and taxa id from assembly accession number
by
GenoMax
129k
There must be some temporary glitch.
Following command works (via EntrezDirect):
$ esearch -db assembly -query GCA_000001405.29 | esu…
Comment: h5ad cellxgene to R
by
abmmki
•
0
matrix=adata.X.toarray()
feature_names = adata.var['feature_name']
pd.DataFrame(data=matrix, index=adata.obs_names, c…
Comment: h5ad cellxgene to R
by
abmmki
•
0
I am trying use the same data and same method. But when I read the csv expression matrix in R, it frozen. Could you share your final seurat…
Comment: h5ad cellxgene to R
by
abmmki
•
0
I am trying use the same data and same method. But when I read the csv expression matrix in R, it frozen. Could you share your final seurat…
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now
by
eimanpharmacist
▴
20
I think the problem in bowtie2 installation. it was installed using this: `conda install -c bioconda bowtie2`
I removed it then re-installe…
Comment: Where to get the molecular subtype information of STAD sample in TCGA
by
Hamid Ghaedi
2.9k
Give `TCGAbiolinks` package a try.
Comment: How to calculate TPM from featureCounts output
by
survive
•
0
hi, So i will need to download the raw .fastq file from SRA and run salmon/Kallisto, instead of using the featureCounts?
Answer: calculate p value and associated z score for snp-gene pair
by
LChart
2.6k
The simplest thing to do would be to 'force' matrixeQTL to output everything by setting `pvOutputThreshold` to 1; this should give you all …
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now
by
eimanpharmacist
▴
20
It is completed but I can not find any bam files, as you see above, I should get a bowtie2.bam file as an output but I did not.
Comment: [Meta] Use of AI
by
GenoMax
129k
It will be up to the people posting the AI assisted/generated comments/answers to add a disclaimer/note line to their posts for now. A butt…
Comment: Is a human genome file with reference as NCBI37 the same as hg19?
by
Ram
39k
Don't cross-post, especially on weekends. It looks like you're in a hurry and you don't care about annoying multiple communities.
Comment: Come work with me! Bioinformatician - Boston MA
by
Joseph
•
0
I am in Boston and my current position Principal Scientist in IHC, in situ Hybridization. I use Bioinformatics but don't have a formal degr…
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
by
GenoMax
129k
Follow your normal analysis protocol. It is possible that your own data could have looked like this. While it is desirable to have upwards …
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
by
Sib
▴
40
Thanks @genomax .I'm trying to do meta analysis of my own.
So, what should we exactly do when we are analyzing a GEO dataset with 30 samp…
Answer: What is the benefit of knowing the source of contamination when we have RNAseq d
by
GenoMax
129k
When one is using public data to do analysis you are likely going to run into this type of situation.
Answer to your question depends on …
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