User: chilifan

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chilifan0
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Posts by chilifan

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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 3 days ago by chilifan0
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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 4 days ago by chilifan0
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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 5 days ago by chilifan0
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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 5 days ago by chilifan0
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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 5 weeks ago by chilifan0
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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 5 weeks ago by chilifan0
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Comment: C: Analyzing digital gene expression data (DGE) from drop-seq pipeline with Seurat.
... Thank you @Igor, got it! :) ...
written 7 weeks ago by chilifan0
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Answer: A: Analyzing digital gene expression data (DGE) from drop-seq pipeline with Seurat.
... Because I like closure I will answer my own question. You need to read in the DGE data before Creating the seurat object. You also need to define column and row names manually and set the data type of data for both the row names (character) and the rest of the data columns (numeric) #Read DGE f ...
written 7 weeks ago by chilifan0
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Comment: A: Analyzing digital gene expression data (DGE) from drop-seq pipeline with Seurat.
... Thank you @Igor that is the answer to a question I've been pondering for a long time. However, ?CreateSeuratObject uses this example: pbmc_raw <- read.table( file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'), as.is = TRUE ) pbmc_small <- CreateSeuratObj ...
written 7 weeks ago by chilifan0
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Analyzing digital gene expression data (DGE) from drop-seq pipeline with Seurat.
... I am using Seurat to cluster data that previously has been filtered, aligned and turned into DGE by the Drop-Seq alignment pipline from Drop-seq tools. This has created a file sample_DGE.txt.gz. I then want to cluster my data and do a QC analysis through calculating the percent mithocondrial genes. ...
R rna-seq seurat written 7 weeks ago by chilifan0

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