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Comment: CuffDiff hangs at same point
by
chavanrenuka852
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hi i have the same issue can you please provide me details how to create small ban file or how to provide subset of bams?
Comment: Script for Rstudio
by
Mensur Dlakic
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28k
I don't think anyone can help you until you tell us the error code.
Answer: blast against Gene Ontology (GO), KEGG, and EuKaryotic Orthologous Group (KOG) d
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Mensur Dlakic
★
28k
Don't know about GO and KEGG, but pretty sure there is no FASTA database for KOG.
BLAST annotation is decidedly old-school, which I don't …
Comment: How to Convert Illumina Final Report File To Plink
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Yan
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Hi there, I have the same problem. did you success using SNPchimpRepo? Thanks!
Comment: GraphAligner/vg surject - alignment output nonsense?
by
stringsAsBaxters
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Did you ever solve this?
GraphAligner doesn't retain the base quality scores in the GAM output, see:
https://github.com/maickrau/GraphA…
Comment: How to represent arbitrarily length kmer?
by
dwpeng
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Hi, rob, thanks to your reply and I wrote a demo in Rust. Repo here: https://github.com/dwpeng/kmer
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
analyst
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Okay thank you so much for making things clear. Raw counts were used for DGE analysis in DESeq2.
Thanks a lot for saving time dsull!
Answer: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
dsull
★
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OK, since you mention you're using DESeq2 for DGE analysis.
DESeq2 uses counts (not FPKMs, not TPMs) for DGE. So if you're using DEseq2 co…
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
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analyst
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Thanks dsull, I am using deseq2 for DGE analysis
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
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dsull
★
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How are you performing the DGE analysis / what tool are you using for it?
Comment: Generating consensus sequence from bam file
by
skdv2522
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Can anyone tell me why there is NNNNNN= no of gaps present in the final fasta file while converting bam into fasta with samtools consensus …
Comment: Generating consensus sequence from bam file
by
skdv2522
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After conversion i got multiple NNNNN in the final fasta file. can anyone tell be why this happens
Comment: How to represent arbitrarily length kmer?
by
dwpeng
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Thank you for the detailed answer. I will read KMC' and cuttlefish's source code.
Comment: GTF file
by
Juke34
8.6k
Have you looked at this issue in GitHub https://github.com/10XGenomics/cellranger/issues/133
If we can catch the sorting issue I could sol…
Answer: Doublets in scRNAseq analysis
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OmnibusX
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I often see a small population of B cells expressing CD3D in scRNAseq data, and I also do find some papers discussing this phenomenon.
I s…
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