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Comment: Question on how to filter DESeq2 results correctly and use of the results functi

Answer: Question on how to filter DESeq2 results correctly and use of the results functi

A: Differential gene expression analysis by DESeq2

The Biostar Herald for Tuesday, March 28, 2023

Comment: What is the NCBI's definition of an "atypical genome"?

Answer: Dealing with very large gene-lists in GSEA

BWA aln returns a smaller number of hits when specifying a higher number of mismatches

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Popular Question to zoukai3412085 • 0

Teacher to barslmn ★ 1.4k

Recent Replies

Comment: What is the NCBI's definition of an "atypical genome"? by GenoMax 127k

You probably need to ask NCBI Help desk for an authoritative answer. Post their response when you get one here.

Comment: How to limit the use of RAM for clustalo? by animeshizik • 0

Hello, thank you for responding to the problem! My work computer has 32GB of RAM. I was running an alignment for a 5000 genome monkey pox…

Comment: Suggestion for approaching multiple conditions scRNA-seq by Eisuan ▴ 20

Hi! Two biological replicates. The previous analysis has been performed on Seurat.

Comment: How to demultiplex single end - dual index run - NextSeq 500 by Apex92 ▴ 260

Thank you.

Comment: genome annotation [sstart] [send] - how to get protein sequence from gene by danfarkas • 0

Hi shenwei356, Thanks for the clarification. That makes sense. I also realised that the reason I was confused, is because I need to also …

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 ▴ 720

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…

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