User: volvicpellegrino

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Posts by volvicpellegrino

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Comment: C: Differential Expression and Co-expression analysis from Cell type-specific datas
... Thanks for your reply, however I don't understand why the microarray threshold can't be used in RNA-Seq? TRAP involves immunoprecipitating GFP tagged ribosomes that are conditionally expressed in a target cell type. There is some non-specific RNA from other cell types, such as astrocytes. I could u ...
written 6 days ago by volvicpellegrino0
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Differential Expression and Co-expression analysis from Cell type-specific datasets
... I use translating ribosome affinity purification (TRAP - the same principle as RiboTag) to extract translating mRNA from a specific cell type, where ribosomes are GFP-tagged. I have an RNA-seq dataset from TRAP-processed samples, that are enriched in genetic markers specific to this cell type. I wan ...
ribotag wgcna deseq2 trap written 6 days ago by volvicpellegrino0 • updated 6 days ago by benformatics490
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Comment: C: Concatenating fastq.gz files across lanes
... Thank you so much to both of you! That makes total sense. ...
written 8 months ago by volvicpellegrino0
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Comment: C: Concatenating fastq.gz files across lanes
... Thanks again, so breaking it down it looks like it lists all files in the directory, truncates the directory values, extracts the 2nd and 3rd fields delimited by '_', sorts them (alphanumerically?), filters matching occurrences, and then runs a concatenate command for every file matching each line o ...
written 8 months ago by volvicpellegrino0
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Comment: C: Concatenating fastq.gz files across lanes
... Thanks very much for this - could you explain how it works or point me in the right direction to understand? ...
written 8 months ago by volvicpellegrino0
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Comment: C: Concatenating fastq.gz files across lanes
... Thanks for your help - the trouble is I have no idea how to specify the right files in a for loop. I understand the principle, its how you construct the code that is the issue. I guess I might have more luck with python. I suppose I could try an os.walk across the directory and a for loop check for ...
written 8 months ago by volvicpellegrino0
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Concatenating fastq.gz files across lanes
... Hi, I have spent several hours trying to figure out the best approach to do this. It would have been quicker to manually do it, but I will need to do this in future. I have 40 paired-end RNAseq samples that were read across 5 lanes. I therefore have 400 fastq.gz files that I would like to process ...
rna-seq written 8 months ago by volvicpellegrino0 • updated 8 months ago by swbarnes24.8k

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Popular Question 5 months ago, created a question with more than 1,000 views. For Concatenating fastq.gz files across lanes

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