User: i.sudbery

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i.sudbery2.5k
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Sheffield, UK
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IanSudbery
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3 years, 6 months ago
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i********@sheffield.ac.uk

Posts by i.sudbery

<prev • 227 results • page 1 of 23 • next >
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Answer: A: How to append the cell barcode and UMI information to the fastq header in paired
... Obviously as the UMI-tools author, I'm going to agree with @Devon Ryan! However, if you really want to do it this way I can think of two options: **Method 1: Extract the the UMI and CB using UMI tools and then reformat the headers. So, using the Biopython SeqIO fastq parser (I'm sure better parsers ...
written 12 days ago by i.sudbery2.5k
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Answer: A: Cuffdiff with 3 conditions
... CuffDiff is outdated software and is no longer best practice (if it ever was). I personally recommend `salmon` or `kallisto` followed by `tximport` and `DESeq2`, although `salmon`/`kallisto` followed by `tximport` and `limma-voom` or `edgeR` or `salmon`/`kallisto` followed by `sleuth` also all work ...
written 4 weeks ago by i.sudbery2.5k
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Comment: C: "Segmentation fault" error from running align function in Rsubread package
... So 'memory not mapped' just means that the application is requesting memory that has not been assigned to any task. The reason for that is not clear from the error - could be poor memory management, or a corrupt input leading to a bad memory request. That your file maps well with TopHat2 suggests ...
written 4 weeks ago by i.sudbery2.5k
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Answer: A: "Segmentation fault" error from running align function in Rsubread package
... Segmentation faults are caused by a program asking for memory at an address that it outside the region allocated to it by the operating system. The two most common reasons for this to happen are: * Running out of memory. I don't know how much memory `Subjunc` (the aligner that `align` calls) uses, ...
written 5 weeks ago by i.sudbery2.5k
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Comment: C: "Segmentation fault" error from running align function in Rsubread package
... Input to align is fastq, not BAM. ...
written 5 weeks ago by i.sudbery2.5k
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Answer: A: What can be considered as novelty in GWAS?
... All you can do with new data is see if new SNPs are identified by it ... Nothing more. What you might be able to do is add your patients as a metaanalysis to existing studies and apply to the meta-analysis that havn't been applied before. Perhaps they are new techniques for correcting for populati ...
written 6 weeks ago by i.sudbery2.5k
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Answer: A: How to convert transcript level TPM to gene level TPM ?
... @harnish is right that Tximport should be able to do transcript to gene level conversion, although I'm not sure if StringTie or express are sources it handle importing form automatically. I've not heard of Tximport calculating TPMs from counts, but I could be wrong. Still, these things arn't hard to ...
written 7 weeks ago by i.sudbery2.5k
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Comment: C: RNASeq DGE : Kallisto-sleuth Vs Ballgown
... I've not really used the ballgown pipeline beyond playing about with it. My own preferred pipeline is `salmon` -> `tximport` -> `DESeq2`, although I can see the conceptual advantages in using `sleuth`. If I want an experiment specific transcript annotaiton, I'll assemble that first with string ...
written 9 weeks ago by i.sudbery2.5k
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Answer: A: RNASeq DGE : Kallisto-sleuth Vs Ballgown
... There are two main differences between the Kallisto-sleuth pipeline and the 'Ballgown' pipeline. Sleuth makes use of Kallisto's bootstrap analyses in order to decompose variance into variance associated with between sample differences and variance associated with quantificaiton uncertainty. I don't ...
written 10 weeks ago by i.sudbery2.5k
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Answer: A: Should bioinformaticians learn the scientific names of plants and animals?
... To add to what others have said, knowing a lot of these is probably not useful, but being able to *recognise* the common ones will probably be helpful (know what they are when you see them, but neccesarily be able to write them yourself). I doubt anyone "learnt" these deliberately, they just become ...
written 10 weeks ago by i.sudbery2.5k

Latest awards to i.sudbery

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 12 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 3 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Popular Question 4 months ago, created a question with more than 1,000 views. For UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
Scholar 4 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 5 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 10 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 10 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 12 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 12 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?

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