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bioinfo-pf-curie / RNA-seq

Nextflow pipeline for RNA-seq pre-analysis (quality controls, genes/isoforms expression, isoform de-novo identification)
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Clarification regarding spike in control #1

Open sbird44 opened 1 year ago

sbird44 commented 1 year ago

Hi, Just wanted to check the normalisation of some of the output files. From the output documentation:

"The number of reads aligned to the spike-in genome are then used to calculate a scaling factor for each sample. This scaling factor will be then applied to generated spike-in normalized bigwig files. Output directory: mapping _spike.bam : Spike-in alignment files Output directory: spike _clean.bam : Alignment file reads aligned on reference genome only *_clean_spike.bam : Alignment file with reads aligned on spike genome only"

Does this mean that only the bigwig file is spike normalised? Is the *_clean.bam file generated after considering the spike in control?

Also is the *filtered.bam is the mapping folder generated after considering the spike in control?

Thanks for your help.

Sarah

nservant commented 1 year ago

Hi @sbird44, Are you sure this is from the RNA-seq pipeline ? and not from the ChIP-seq one ?

sbird44 commented 1 year ago

Hi,

I’m so sorry yes this is in reference to the CHiP-Seq pipeline https://github.com/bioinfo-pf-curie/ChIP-seq/blob/master/docs/output.md

Thanks,

Sarah

From: Nicolas Servant @.> Sent: 17 April 2023 14:35 To: bioinfo-pf-curie/RNA-seq @.> Cc: Sarah Bird @.>; Mention @.> Subject: Re: [bioinfo-pf-curie/RNA-seq] Clarification regarding spike in control (Issue #1)

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Hi @sbird44https://github.com/sbird44, Are you sure this is from the RNA-seq pipeline ? and not from the ChIP-seq one ?

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