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Recent Replies
Comment: Mapping all 32-mers within Hamming Distance = 3
by
GenoMax
123k
If you are mapping then why are you using `bbduk.sh`? You should use `bbmap.sh` instead. Why are you exporting the result as a `.fq` file?
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene
by
Matthias Zepper
2.4k
You are missing, that the IDs are not 1:1 mappings. Refseq, Entrez Gene and Ensembl are separate corpuses of human genome annotations and s…
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene
by
mbansal
•
0
Thanks. I have updated the post. Can I add input data if anyone wants to replicate the issue I am having?
Comment: snpeff : wont recognize the gtf or gff3 files (runtime exception)
by
Kaavya
•
0
I have the exact same issue with introduction of '.' between directories, will it be solved with changing admin privileges?
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene
by
GenoMax
123k
Please do not post screenshots (use text and `101` button to format that as `code`). Screenshots do not allow people to copy text for testi…
Comment: minimap2, before or after assembly?
by
emiliomastriani
▴
30
You are right. I am sorry to have been not so clear.
Dataset: we have a collection of fast5 files from Nanopore MinION, in total 10 barcode…
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene
by
mbansal
•
0
Hello,
I am trying to convert RefSeq ids to gene symbols using the biomaRt R package. I followed the below script to align the input entrie…
Comment: Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me
by
Matthias Zepper
2.4k
In my perception, there should be little difference between narrow peak annotation and broad peak annotation? I and others have used Homer'…
Comment: Package installation error using Bioconda
by
Dunois
★
2.2k
Did you try specifying the channel explicitly like so `conda create -n antismash -c bioconda antismash`?
If not, it's worth trying out `ma…
Comment: Which hit do I select from my BLASTN result when all of them have the same stati
by
Dunois
★
2.2k
The top 10 hits are all OXA genes, and the matches are all significant, high subject coverage, and high identity. But the query coverage is…
Comment: Which hit do I select from my BLASTN result when all of them have the same stati
by
GenoMax
123k
Please do not delete posts once they have received at least one comment/answer. While you may have resolved your question this thread may h…
Comment: disagreement between edgeR logFC and readCounts submitted
by
bhanu.chandra1
▴
50
Hi,
I could not figure it out with edgeR. I was reading multiple posts suggesting NOISeq as an option to analyze the "no replicate" data. T…
Comment: Package installation error using Bioconda
by
manaswwm
▴
270
have you tried using [mamba][1] within conda to install packages, it is relatively faster and easier to identify trouble causing dependenci…
Comment: Running nf-core rnaseq with smart-seq3 data
by
firestar
★
1.4k
A colleague has referred me to the [zUMIs](https://github.com/sdparekh/zUMIs) pipeline which handles all scRNASeq data from 10X to smart-se…
Answer: STAR Aligment Running Problem
by
GenoMax
123k
Looks like this file `/truba_scratch/sbuyukkilic/rnaseq//genomeParameters.txt` does not exist. As you can see STAR is not able to read/find…
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