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

Comment: How to demultiplex single end - dual index run - NextSeq 500

Heatmap deseq2

A: Extract Base Based On Position From Bam File

PyComplexHeatmap: a Python package to visualize multimodal genomics data

pulling snps from vcf file using ids

A: pulling snps from vcf file using ids

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Popular Question to zoukai3412085 • 0

Teacher to barslmn ★ 1.4k

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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 ▴ 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…

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