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Answer: Scaling RNA-Seq data before clustering?
Answer: How to use CAFE from Orthofinder Results
Answer: merge vcf.gz file
STAR solo set parameters for scrna-seq
STAR solo set parameters for scrna-seq
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Comment: mpileup to sync file
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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
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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```…
Comment: differential gene analysis
by
kalyani
• 0
okay thankks!
Comment: Kallisto bustools for scRNA-seq
by
t.ru
▴ 20
@SRR17050039.1 NB501465:544:HF2H7BGXB:1:22104:14442:1233_TCCTGAGC_barcode=NA-EEEE-AAAAAEE-EEEEEEEE-GCTG-TGCCAGA-ACGTTCAT-W202012/1 GCCCTGTA…
Comment: merge vcf.gz file
by
Pierre Lindenbaum
153k
"file 1 " , with a space, cannot be a real argument. show us the real filenames please, and the error messages.
Answer: merge vcf.gz file
by
ATpoint
70k
You must compress with bgzip. gzip -d your.vcf.gz bgzip your.vcf
Comment: GO enrichment analysis
by
hellokwmin
• 0
Thank you for your reply. Unfortunately, the organism I am using is non-model organism (i.e. one of plant species). So, with the informati…
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