User: i.sudbery

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i.sudbery1.0k
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IanSudbery
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Posts by i.sudbery

<prev • 118 results • page 1 of 12 • next >
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Answer: A: Existing software to calculate RNASeq read distribution by "gene_type" (Gencode)
... You should be able to do this with [CGAT][1]. Briefly you want to prepare a bed file where the name column of the bed is taken from the gene_type attribute of the GTF. You can do this with cgat gtf2bed --set-name=gene_biotype -I gencode.gtf.gz -S gencode_gene_type.bed.gz You can then use `c ...
written 1 day ago by i.sudbery1.0k
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Answer: A: Finding miRNA promoter in UCSC genome browser?
... The primary transcripts for miRNAs are often not annotated - that is we often don't really know what they are. One reason for this is that they are unstable, and so unlikely to be picked up in cDNA/EST libraries. Other than the the mature miRNA, they are often not conserved either, so they can't be ...
written 1 day ago by i.sudbery1.0k
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Answer: A: TCGA genotype data
... All data for TCGA is now accessed through the Genomic Data Commons data portal: https://gdc-portal.nci.nih.gov/ If you select data and then select the "Files" tab you can select "Genotyping Array" as the data type. However, it appears in the main data portal only copy number variation is available ...
written 23 days ago by i.sudbery1.0k
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Comment: C: Normalisation of arrays with global changes expected
... Just to report back on this... Rank invariant normalisation does in fact do better than something like quantile normalisation, but it is still clearly normalising away real differences, as can be seen by the behavoir of spike-in controls. Unfortunately normalising to the spike-ins doesn't work eithe ...
written 28 days ago by i.sudbery1.0k
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Answer: A: Error: duplicate GFF ID 'ENST00000400518' encountered! [FAILED] Error: c
... Could well be a GTF that is not sorted in the correct order. I don't know how the cufflinks parser works, but for many GTF parsers, duplicate IDs are detected by finding that exons the same ID are not all next to each other. This can happen if the file is sorted purely on chromosome and start positi ...
written 28 days ago by i.sudbery1.0k
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Comment: C: Opinion: Bioinformatician - What comes first? Biology vs Informatics.
... The corollary to this is that if you are a informatician first, you'll struggle not to spend all your time answering other peoples requests rather than guiding your own work. ...
written 6 weeks ago by i.sudbery1.0k
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Comment: C: Normalisation of arrays with global changes expected
... We are looking at RNA processing genes, so there is no reason to suspect that "housekeeping" genes wouldn't also be affected, but I'll look into the rank invariance thing. ...
written 7 weeks ago by i.sudbery1.0k
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Comment: C: Normalisation of arrays with global changes expected
... Its human 293 cells. The data are single channel, so no dye swaps i'm afraid. ...
written 7 weeks ago by i.sudbery1.0k
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Normalisation of arrays with global changes expected
... I've picked up an analysis that has been sitting in someone's drawer for a while. Its an Agilent array experiment where global changes are expected between the control and the treatment. The person who originally did the analysis (on GeneSpring :( ) stated in their material and methods that they use ...
microarray normalisation limma written 7 weeks ago by i.sudbery1.0k • updated 7 weeks ago by patrick.bradley30
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Comment: C: The right pipline with cufflinks, cuffmerge and cuffdiff
... Yeah, I'm pretty sure the input requirements are the same as cufflinks. ...
written 7 weeks ago by i.sudbery1.0k

Latest awards to i.sudbery

Popular Question 12 days ago, created a question with more than 1,000 views. For StringTie: To use a reference gene-set or not?
Scholar 23 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Appreciated 27 days ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Guru 27 days ago, received more than 100 upvotes.
Centurion 11 weeks ago, created 100 posts.
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 5 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Alternative to Cufflinks ?
Scholar 7 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 7 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Alternative to Cufflinks ?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 7 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 7 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?

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