User: GSAENZDEPIP

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GSAENZDEPIP10
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Posts by GSAENZDEPIP

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Question about deduplication with UMI-tools
... **This was the answer from Tom Smith** (Github): Hi @gsaenzdepip. Your picard MarkDuplicates command ignores UMIs. Thus, two reads with the same alignment coordinates with be considered duplicates even if they have different UMIs. The duplication rates you have obtained are therefore over-estimates ...
written 29 days ago by GSAENZDEPIP10
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Comment: C: Question about deduplication with UMI-tools
... I did not use "UMI-tools count" because I want to use HTSeq for counting. I simply use the output BAM file (from STAR aligner) as the input for "UMI-tools dedup" in order to obtain a BAM file without duplicates. Then I want to use that BAM file without duplicates for counting with HTSeq. Thank you ...
written 4 weeks ago by GSAENZDEPIP10
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Question about deduplication with UMI-tools
... Hello, I am using UMI-tools for deduplicating some RNA-seq samples. I have high duplication levels due to the protocol used for library generation. However, after using UMI-tools the duplication levels are still higher than 20% in all the samples. Is this normal or I should change some UMI-tools par ...
umi rna-seq written 4 weeks ago by GSAENZDEPIP10 • updated 4 weeks ago by genomax54k
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Comment: C: Bcl2fastq avoid addition of barcode to header
... It worked!! Thank you very much ...
written 4 weeks ago by GSAENZDEPIP10
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Comment: C: Bcl2fastq avoid addition of barcode to header
... Okey, I will try UMI-tools without removing the barcode and see if it works. Thanks! ...
written 5 weeks ago by GSAENZDEPIP10
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Bcl2fastq avoid addition of barcode to header
... Hello, I am demultiplexing some samples with bcl2fastq and I wonder if it is possible to avoid the addition of the barcode sequence to the header of the reads. Many thanks, Goren P.D: In the next steps I will use UMI-tools for adding the UMI sequence to the header, so I need to get rid of the barc ...
rna-seq written 5 weeks ago by GSAENZDEPIP10 • updated 5 weeks ago by swbarnes23.9k
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Comment: A: Batch effect removal (Combat)
... Thank you! I have just found the answer in the tutorial: "For sequencing data, which are often represented as counts, a more suitable model may involve the use of a moderated log function" ...
written 4 months ago by GSAENZDEPIP10
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Batch effect removal (Combat)
... Hi! I want to remove batch effect from a count data matrix (RNAseq experiment) using Combat function (sva package). I know that RemoveBatchEffect function (from Limma package) needs Log-transformed input, however Combat manual doesn't mention whether input data should be Log-transformed... Thank yo ...
rna-seq written 4 months ago by GSAENZDEPIP10

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