User: user31888

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user3188860
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Posts by user31888

<prev • 73 results • page 1 of 8 • next >
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Comment: C: Divergent number of replicates between FastQC and samtools
... Thanks for your explanation. It's a bit out of the topic here, but I am just curious. According to you, if one have single-end reads, fastqc and samtools / picard / STAR should output the same number of duplicates then? ...
written 6 weeks ago by user3188860
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Comment: C: Divergent number of replicates between FastQC and samtools
... Thanks for your very complete answer ! I actually did use `--bamRemoveDuplicatesType UniqueIdentical`, but my version of STAR (2.5.1b) does not tag duplicates in the same time as aligning fastq reads. I needed to (1) align the .fastq reads; (2) tag duplicates using `star --runMode inputAlignmentsFro ...
written 6 weeks ago by user3188860
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Comment: C: Divergent number of replicates between FastQC and samtools
... Correct. After counting them all "manually", I found a different number as well. ...
written 6 weeks ago by user3188860
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Divergent number of replicates between FastQC and samtools
... I have a total of 300 million reads in my R1 and R2 raw fastq files. How come fastQC count about 50% duplicates in each .fastq files, but after alignment with STAR (default parameters), none of the reads have the 1024 flag (PCR or optical duplicates) when doing `samtools view -c -f 1024 mydata.bam` ...
samtools star fastqc written 6 weeks ago by user3188860 • updated 6 weeks ago by i.sudbery5.0k
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Comment: C: Normalisation of reference dataset for scRNA cell type annotation
... I came across this recent [database][1], CellMarker. Do you think a simple GSVA using this database could be accurate? I need to get a score of some sort to be able to discriminate cell types. [1]: http://biocc.hrbmu.edu.cn/CellMarker/index.jsp ...
written 11 weeks ago by user3188860
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Comment: C: Normalisation of reference dataset for scRNA cell type annotation
... Do you mean using cell type signatures and scoring their enrichment with GSEA or gsva for example? ...
written 11 weeks ago by user3188860
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Normalisation of reference dataset for scRNA cell type annotation
... I have scRNA data in a form of a `SingleCellExperiment` object that I previously filtered, normalised, clustered, with genes selected. I am trying to assign a cell type to each of my cells in this `SingleCellExperiment` object using `scmap` ([here][1]) and the [Human Primary Cell Atlas][2] (HPCA) a ...
scmap human primary cell atlas scrna cell type written 11 weeks ago by user3188860
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Comment: C: Demultiplexing single cell QIAseq UPX 3 Transcriptome Kits fastq files
... Ok, I did not know. I removed the sequences from my original post (although it could have been useful for other people). ...
written 3 months ago by user3188860
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Comment: C: Demultiplexing single cell QIAseq UPX 3 Transcriptome Kits fastq files
... I got the 10 base-long cell_ID sequences (see edit) and UMI = 12 bases long. Everything work just fine now. Thanks ! ...
written 3 months ago by user3188860
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Comment: C: Demultiplexing single cell QIAseq UPX 3 Transcriptome Kits fastq files
... Thanks for your help ! I just need to figure out the length of the cell barcode and UMIs now. ...
written 3 months ago by user3188860

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