User: chilifan

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chilifan60
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Posts by chilifan

<prev • 14 results • page 1 of 2 • next >
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Singe cell identification library with Ensembl_ID:s
... I am analyzing some gene/cell expression data tor try to annotate the cell type using SingleR. My data is from 10x and consists of two columns that serve as row names, one ensemble Gene_ID and one symbol, for example CYTH3. The data look like below: Gene_ID Symbol AAACCTGCACACTGCG.1 AAA ...
haplotypes ensembl gene_id library annotation written 25 days ago by chilifan60
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Principal component analysis: PC2 contribute more to variance than PC1?
... I am clustering data using Satija's Seurat package. Link: https://satijalab.org/seurat/pbmc3k_tutorial.html Now I'm doing a presentation about principal component analysis (PCA). As I've understood it, the dimensions that contribute with the highest variance to the dataset is used for the first prin ...
pca principal component analysis seurat written 5 weeks ago by chilifan60 • updated 5 weeks ago by manuel.belmadani570
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Comment: C: Clusters moving for same dataset and code using tSNE
... Thank you, this makes perfect sense:) I am indeed using another method for clustering, so I conclude that I can trust the cell identities of my clusters then. ...
written 5 weeks ago by chilifan60
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Clusters moving for same dataset and code using tSNE
... I am clustering data using Satija's Seurat package. Link: https://satijalab.org/seurat/pbmc3k_tutorial.html I am using this exact code and their data, and I generate the same plots as them. However, visualiizing my clusters with tSNE, they are positioned differently compared to the example on satija ...
tsne clustering scrnaseq seurat written 5 weeks ago by chilifan60 • updated 5 weeks ago by i.sudbery4.1k
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Chromosome disagreement in drop-seq meta data pipeline
... I am generating meta data and genome index for h. sapiens through the drop-seq 2.0.0 pipeline called create_Drop-seq_reference_metadata.sh. I have tried using fasta reference and GTF files from both ensamble! and gencode (https://www.gencodegenes.org/human/ using the Genome sequence (GRCh38.p12) fa ...
drop-seq rna-seq meta data genome indexing written 9 weeks ago by chilifan60
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Comment: C: SO:coordinate Error parsing text SAM file. Line: BAM#Pm@HD VN:1.5 SO:coordinate
... Hi @finswimmer thank you for your reply. I started the drop-seq pipeline, but it had an error just before the last step, so I restarted the last step. That is, the first files in the pipeline are generated from this code: >>/home/path/to/tools/Drop-seq-1.12/Drop-seq_alignment_DS.sh -g /ho ...
written 9 weeks ago by chilifan60
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Comment: A: BBDuk.sh and BBDuk2.sh barcodefilter does not filter the reads
... All of the above comments are correct, my sample has already been demultiplexed and the barcode is fetched by grep in the sequence. hence, I don't need to use BBDuk2.sh to filter for my barcode. Thank you for your help! :):):) ...
written 9 weeks ago by chilifan60
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SO:coordinate Error parsing text SAM file. Line: BAM#Pm@HD VN:1.5 SO:coordinate
... I've processed some scRNA data from raw reads to clustering and used Drop-seq tools for a part of the processing (the drop-seq pipeline rely partly on picard tools as well). The processing went without trouble, but now when I want to go back and revise my processing and do some extra quality checks, ...
drop-seq pipeline samtools bam file written 9 weeks ago by chilifan60
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Comment: A: BBDuk.sh and BBDuk2.sh barcodefilter does not filter the reads
... hm, well, yes with grep I *want* to count the existance of the barcode sequence. It's just my way of checking that the barcode actually exists and that I should filter on barcode for col02, rather than filtering on any of the rest of the barcodes for other columns. I base that on the number of reads ...
written 3 months ago by chilifan60
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BBDuk.sh and BBDuk2.sh barcodefilter does not filter the reads
... I have a sample from illumina I want to filter so that only the reads containing the barcode TAAGGCGA are kept in an output file. I know that this barcode exists and that I have contamination from other barcodes through this bit of code: #Barode for COL02 $ grep TAAGGCGA R1.fastq | wc -w ...
barcode fastq bbduk bbmap illumina index written 3 months ago by chilifan60

Latest awards to chilifan

Student 5 weeks ago, asked a question with at least 3 up-votes. For Clusters moving for same dataset and code using tSNE

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