User: GSAENZDEPIP

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GSAENZDEPIP10
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6 months, 1 week ago
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G**********@ALUMNI.UNAV.ES

Posts by GSAENZDEPIP

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Analysis of GEO dataset normalized by FPKM
... One last question. The raw data of these project has 3-4 runs per sample... how should I deal with it? I have always worked with one .fastq file per sample. Is there any tutorial for this situation? Thanks! ...
written 4 weeks ago by GSAENZDEPIP10
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Comment: C: Analysis of GEO dataset normalized by FPKM
... Okey, I will do it from raw data. I didn't know that you could download RNAseq experiments from ENA... Thank you!! ...
written 4 weeks ago by GSAENZDEPIP10
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Analysis of GEO dataset normalized by FPKM
... Good morning, I'd like to perform differential expression analysis with some RNA-seq samples from GEO database (GSE99987) and obtain significant genes between different conditions. However, the count tables that are available on GEO show FPKM normalized counts. This normalization was done by Cuffdi ...
rna-seq written 4 weeks ago by GSAENZDEPIP10
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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 12 weeks 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 12 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 12 weeks ago by GSAENZDEPIP10 • updated 12 weeks ago by genomax57k
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Comment: C: Bcl2fastq avoid addition of barcode to header
... It worked!! Thank you very much ...
written 3 months 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 3 months 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 3 months ago by GSAENZDEPIP10 • updated 3 months ago by swbarnes24.2k
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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 6 months ago by GSAENZDEPIP10

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