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Recent Replies
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…
Answer: Which hit do I select from my BLASTN result when all of them have the same stati
by
GenoMax
123k
What database are you blasting against? Clearly there is a lot of redundancy in that database which is why you get nearly identical hits fr…
Answer: Which hit do I select from my BLASTN result when all of them have the same stati
by
Istvan Albert
96k
Sounds like your subject sequences are identical - the data might be redundant.
In any case, you should reverse the question instead - …
Answer: Why multiple SYMBOLS, Consequences... for Variant Effect Predictor (VEP)
by
barslmn
▴
30
Ensembl VEP annotates for every allele, gene and transcript. You can flag or pick alleles or transcripts with pick options.
https://ww…
Comment: Running nf-core rnaseq with smart-seq3 data
by
ATpoint
66k
SMART-seq is a plate-based assay. Each well of the plate is a cell, and each cell has its own fastq file. This is not like 10x Chromium whe…
Answer: multiqc hisat2 question
by
Phil Ewels
★
1.0k
You can find details of how MultiQC finds outputs in the documentation. For example, HiSAT is [here][1] and is as follows:
```yaml
kall…
Comment: Running nf-core rnaseq with smart-seq3 data
by
Phil Ewels
★
1.0k
I'm not sure if you're the same person or not, but we're having an almost identical conversation on the nf-core Slack at the moment [ [link…
Comment: Can't convert SRA to FASTQ with fasterq-dump. fasterq-dump was killed (signal 9
by
Amitm
★
2.1k
Hi,
If I've understood correctly the log then the scratch space (tmp) is in your home dir. There is a parameter (I think `-t` ) that could …
Comment: Can't convert SRA to FASTQ with fasterq-dump. fasterq-dump was killed (signal 9
by
hazirliver
▴
10
Thank you! I think this is the best solution for my task
Comment: Plotting HiChIP data without Sushi in R
by
Matthias Zepper
2.4k
I used the [Gviz][1] packageto plot [genomic regions for my thesis][2] in R. However, despite many default [TrackClasses][3], the library l…
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