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kenneditodd
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predeus
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Recent Replies
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴
280
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 ?
by
Phil Ewels
★
1.2k
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…
Comment: Problem with GPU guppy_basecaller and SLURM
by
kenneditodd
▴
10
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…
Comment: Where to get the molecular subtype information of STAD sample in TCGA
by
younglin113
▴
50
Thanks a lot! But still a bit curious why this information is not included in GDC or UCSC xena.
Comment: CellRanger problem
by
Carlos Eduardo
•
0
I'm using cellranger mkref --genome=Viral --fasta=path.fna --genes=path.gtf
I have 126G RAM
Comment: How do I run DE for TPM values (not CPM)?
by
John
•
0
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)?
by
LChart
2.7k
you're mixing two packages, edgeR ("dgelist") and limma ("lmFit"). Just put your log(1+TPM) matrix as the first argument to lmFit.
Answer: hisat2-align exited with value 1
by
GenoMax
130k
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
by
Andy
▴
50
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
by
Ram
39k
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
by
Jeremy Leipzig
21k
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
by
Ram
39k
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
by
Ram
39k
> 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)?
by
John
•
0
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.
Answer: no output from GATK CombineGVCFs
by
Vitis
★
2.5k
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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