User: slapiiv

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slapiiv50
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11 months, 2 weeks ago
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3 years, 1 month ago
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Posts by slapiiv

<prev • 12 results • page 1 of 2 • next >
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Answer: A: know the grep command for fastq file
... grep 'HISEQ:151:HHKH7BCXX:2:1203:18952:80029' your_fastq_file.fastq ...
written 11 months ago by slapiiv50
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Comment: C: How to proceed after removing batch effect with limma?
... Thanks Pietro, I have found the answer: dds <- DESeq(dds, test="LRT", reduced=~batch) ...
written 12 months ago by slapiiv50
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Comment: C: How to proceed after removing batch effect with limma?
... Thanks h.mon, so, basically I just can remove it for visualization but not for the calculation of DE? ...
written 12 months ago by slapiiv50
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How to proceed after removing batch effect with limma?
... Hi everyone, I have visualized some batch effects in my sequencing replicates and I have removed with the limma package as follows. mat <- limma::removeBatchEffect(mat, vsd$batch) After that, batch effect has been at least minimized and the PCA looks very good as I expected, however, at thi ...
batch-effect deseq2 limma rna-seq written 12 months ago by slapiiv50 • updated 12 months ago by Pietro100
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Comment: C: bowtie --best, what exactly does it mean?
... Oh I see, bowtie is a bite confusing anyways, but I have undesrstand my specific doubt. Thanks. ...
written 15 months ago by slapiiv50
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Comment: C: bowtie --best, what exactly does it mean?
... Thanks, the answer that I was looking for is: a strata is a set of alignments where mismatches occur at identical positions. For example, suppose there are two 1-mismatch hits. One with the mismatch at 7th position and the other at the 9th position. The two hits are in two different strata. ...
written 15 months ago by slapiiv50
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Comment: C: Dual rnaseq normalization
... Nice, I will take a look but it seems very useful, thanks. ...
written 15 months ago by slapiiv50
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bowtie --best, what exactly does it mean?
... Hi, everybody: I am using bowtie for aligning smallRNAseq reads against a genome reference, I am using *--best* because it is recommended for miRNAs, but as you may know the bowtie`s manual is not clear enough as we the beginners need. Does somebody know what does it exactly means? --best ...
bowtie rna-seq mapping written 15 months ago by slapiiv50 • updated 15 months ago by Charles Warden7.8k
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Dual rnaseq normalization
... Hi everybody, I have performed a dual rnaseq (infected cells by a pathogen) at different points, at the beginning host-corresponding reads are more than 90% of the total, however, at a later point, I have almost 50% or reads corresponding to the host and 50% corresponding to the protozoo (total rea ...
normalization rna-seq written 15 months ago by slapiiv50 • updated 15 months ago by grant.hovhannisyan2.0k
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Comment: C: Find number of rows contain zero raw count across all sample (column) using R
... If my answer was helpful you should upvote it, ...
written 3.1 years ago by slapiiv50

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Supporter 2.2 years ago, voted at least 25 times.

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