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Recent Replies
Comment: GTF file for Rhinolophus sinicus
by
atowns21
•
0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome.
[1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
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yxwucq
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The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
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Mensur Dlakic
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There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
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atowns21
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Hmm, okay I'm not sure what is going on, but here is what I did:
1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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HyperEvo
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Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
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I have 2 files output, no error logs...
the .kreport file: 100.00 160136511 160136511 U 0 unclassified
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Comment: TCGA2STAT Error: Firehose connection
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LauferVA
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agree.
from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
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yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
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This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
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Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
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We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
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Let us know when you find out. Would be a useful thing to know what the data looks like.
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
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atowns21
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Yes, that is a very good idea. Thanks for the help!
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
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GenoMax
141k
Only thing would be to try them out. See if you can detect them in the data you have.
You could also simply look for unique representativ…
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