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Popular Question to
Anand Rao
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Fizzah
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Ben_Ensembl
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Recent Replies
Comment: Suggestion for approaching multiple conditions scRNA-seq
by
rpolicastro
11k
Do you have 2 biological or technical replicates for each condition? Also, you mentioned you didn't find dramatic changes with your analysi…
Comment: GO enrichment analysis
by
Antonio R. Franco
★
5.0k
I had the same situation that I solved using the R package TopGO.
You have already the list of GO terms. Need to follow the instructions i…
Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
by
andres.firrincieli
3.1k
Hi @6f8262bb
I still have no idea what could be the cause but switching to guppy v6.2 solved this problem
Answer: Dealing with very large gene-lists in GSEA
by
Trivas
▴
710
IMO, in those cases you could look at ES instead of NES. Regardless, within the function `fgsea`, you can set the parameters `minSize` and …
Comment: merge vcf.gz file
by
Mali
•
0
file1 = '/sci/labs/orzuk/orzuk/projects/Skin/data/Ichilov/vcfFiles/vcfFiles/eb3_1001_748-gatk-haplotype.final.vcf.gz'
file2 = '/sci/labs/or…
Comment: Which GPU for local Colabfold
by
matt_arnold_bio
•
0
Another giveaway is that when you hit run, it will say either "Running on GPU" or "Running on CPU" in the log output...
![enter image desc…
Answer: Which GPU for local Colabfold
by
matt_arnold_bio
•
0
Hi Arjen,
This is a little while ago now so maybe this is not that helpful but...
You should be able to tell if the GPU is being seen…
Comment: STAR solo set parameters for scrna-seq
by
t.ru
▴
20
it's single cell mars-seq. Yes sorry its a fastq file.
Answer: boxplot issue
by
yura.grabovska
▴
50
First of all, you're not outputting the result of your scale to anything...
t(apply(mat, 1, scale))
colnames(mat) <- rownames(cold…
Comment: STAR solo set parameters for scrna-seq
by
GenoMax
127k
> a fasta file similar to this
This is not a fasta file It is a fastq format file.
Are you sure this is single cell RNAseq data? Looking…
Answer: heatmap issue
by
yura.grabovska
▴
50
Your controls clearly show variable expression for the genes you're plotting so to get them to stick together on the left, you would need t…
Comment: How to demultiplex single end - dual index run - NextSeq 500
by
GenoMax
127k
Correct. This is a single-end dual indexed (8 bp each) run.
Comment: genome annotation [sstart] [send] - how to get protein sequence from gene
by
danfarkas
•
0
Hi shenwei356,
Thanks for the clarification. However, I did try this, and it was not yielding the expected amino acid sequences. This is w…
Comment: Artificial reads - remove multiple mapped reads against reference genome, and on
by
Agamemnon
▴
60
I ran ```samtools view -F 4 -q 42 test.bam | wc -l``` and I get ```6159141```, why is there a discrepancy, as originally only ```5200484```…
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