User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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Comment: C: Downsampling one of the sample on the UMAP clustering to match the number of cel
... Yes, the collaborator requested equal number of cells on both the WT and KO samples. This is what I expected initially equal number of cells in each conditions under each cluster as well. The below image is based on the dummy data I manually entered. But in the above image actual KO value vs down ...
written 6 weeks ago by bioinforesearchquestions280
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Comment: C: Downsampling one of the sample on the UMAP clustering to match the number of cel
... Yeah I tried the approach2. WT_cells <- which(WT_KO_integrated_seurat$sample == 'WT') KO_cells <- which(WT_KO_integrated_seurat$sample == 'KO') downsampled_KO_cells <- sample(KO_cells, 895) WT_KO_integrated_downsampled <- WT_KO_integrated_seurat[,c(WT_cells, downsa ...
written 6 weeks ago by bioinforesearchquestions280
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Comment: C: How many PCs should be considered for downstream analyses?
... Thanks, Mensur for adding a point. Can you please look into this post of mine related to this analysis? https://www.biostars.org/p/423349/ ...
written 6 weeks ago by bioinforesearchquestions280
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Downsampling one of the sample on the UMAP clustering to match the number of cells of the other group
... Hi friends, I have two groups WT and KO. I have roughly 950 cells in WT sample and 1700 cells in KO sample. As I mentioned in this post https://www.biostars.org/p/423306/#423337. Steps followed for the analyses: - Individual seurat object for WT and KO - Merged WT_KO - Filtered_WT ...
rnaseq scrnaseq umap downsampling written 6 weeks ago by bioinforesearchquestions280 • updated 6 weeks ago by jared.andrews075.3k
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Comment: C: How many PCs should be considered for downstream analyses?
... Can you please look into this post of mine related to this analysis? https://www.biostars.org/p/423349/ Thanks Jared for your comments and resources. I was playing around by changing the number of PCs from 15 to 40. I have attached them below for reference. The overall clustering pattern didn't c ...
written 6 weeks ago by bioinforesearchquestions280
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How many PCs should be considered for downstream analyses?
... Hi All, I have two groups WT and KO. As per the Jackstraw plot, ‘Significant’ PCs will show a strong enrichment of features with low p-values (solid curve above the dashed line). 1. How to interpret the JackStraw plot. How come even the PCs with p-value =1 is above the dashed line. 2. PC 5 has p ...
rnaseq scrnaseq pca umap clustering written 6 weeks ago by bioinforesearchquestions280 • updated 6 weeks ago by jared.andrews075.3k
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How to find percentage of a gene (eg.Ppbp) for condition A and condition B from 10X Single Cell RNAseq?
... Hi All, I am working on a single cell rnaseq dataset for two conditions. 10X genomics protocol and Novaseq platform was used to sequenced the single cells. BCL to FASTQ has been performed. Then I ran cellranger count pipeline on those FASTQ files to get the output files. As per the summary, - Con ...
rnaseq 10x single cell cellranger written 3 months ago by bioinforesearchquestions280 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... I annotated both the contigs.fasta using PROKKA. Then I used the isolateA.gbk and isolateB.gbk for generating the mauve output. Then I tried reordering the contigs using the isolateA.gbk and isolateB.gbk. Brigs output online coin flip simulator ...
written 7 months ago by bioinforesearchquestions280
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... Hi genomax, As discussed, the isolateA (denovo assembly carried out) assembled contigs.fasta has been used as the reference and created the required index files. Then the FASTQ files of isolateB has been aligned against the isolateA contigs.fasta (reference) using BWA. Then using callvariants.sh I ...
written 7 months ago by bioinforesearchquestions280
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... This is the error There was a problem with the search. Please, contact Help Desk and include RID P07DS4TZ01R Informational Message: [blastsrv4.REAL]: Error: Process size limit exceeded, resulting in SIGXFSZ (25). ...
written 7 months ago by bioinforesearchquestions280

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