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Differences between trimming tools: cutadapt, bbduk and sickle
C: How sickle (adaptive trimming tool) work.
How sickle (adaptive trimming tool) work.
Comment: Help with running ATAC using Encode pipeline
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
A: Can EdgeR of DeSeq be used for Single-cell RNA-seq?
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Comment: GISTIC from ASCAT
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Hyper_Odin
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Hi, Ram thanks for the help...I figured out the issue. somehow I had duplicate files in the folder which caused the issue.
Answer: multiqc: group samples by population + boxplot ?
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Phil Ewels
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You can't group and make boxplots as you describe, probably your best bet is to use the [highlight tool][1] in the report (especially if yo…
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Nope - but I just noticed another error message in the guppy log. I've seen some people have the same problem on nanopore community but not…
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Thanks a lot! But still a bit curious why this information is not included in GDC or UCSC xena.
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I'm using cellranger mkref --genome=Viral --fasta=path.fna --genes=path.gtf I have 126G RAM
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John
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Thanks, but it's giving me the error that expression object should be numeric and that there are 2 non-numeric columns (because the first t…
Comment: How do I run DE for TPM values (not CPM)?
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LChart
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you're mixing two packages, edgeR ("dgelist") and limma ("lmFit"). Just put your log(1+TPM) matrix as the first argument to lmFit.
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You only need to use the `basename` of the index when you specify it. Try hisat2 -p 4 -x /home/ngs/zebra_fish/zebra_fish -U SRR10480…
Comment: How to deal with SRA file without .SRA
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Andy
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Thank you Ram! Yes, I did something wrong.
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
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Ram
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Exactly. Even when we were trying to leverage hail at my previous job, we ran into troubles constantly with data freezes. IMO academia is n…
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
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Jeremy Leipzig
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OK hospitals in particular definitely don't want to regenerate anything as individual new samples are added to the variant store. Even the …
Comment: How to deal with SRA file without .SRA
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Ram
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PRJNA is the standard NCBI BioProject prefix. There are 19 pairs of FASTQs associated with this one so you're doing something wrong
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
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Ram
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> But you can't live out of your suitcase forever. I'd compare it to a local department store vs Walmart - I think cloud/distributed stora…
Comment: How do I run DE for TPM values (not CPM)?
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John
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That's what I'm trying to do but again, I'm getting an error on the last line and I'm asking how to fix it.
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Vitis
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The number of gVCFs in the list has a hard limit (interestingly I don't exactly know this number as it changes with different GATK versions…
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