User: i.sudbery

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i.sudbery2.7k
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Sheffield, UK
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IanSudbery
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i********@sheffield.ac.uk

Posts by i.sudbery

<prev • 241 results • page 1 of 25 • next >
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Comment: C: limitations of Edge R or DEseq
... " to see DE among large number of samples". Sounds like you have replicates to me. See my answer here: https://www.biostars.org/p/292316/#292418 ...
written 6 days ago by i.sudbery2.7k
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Comment: C: % of reads unmapped: too short - STAR 2.5.2b
... % reads unmapped: Too short is what you get when your read just don't map: If a read doesn't map, STAR will clip bases off the end of the read until either the read maps, or it is too short. So STAR is just saying that it can't map the reads. We recently had a similar problem where STAR wouldn't map ...
written 7 days ago by i.sudbery2.7k
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Answer: A: De-duplicate UMI at FASTQ level
... I know of no tool that can do does this, and there are probably good reasons for that. In the case of most protocols that use UMIs, **the UMI alone simply isn't unique enough to uniquely identify a pre-PCR molecule**. Consider: For deduplicating only on a UMI to work, it has to be far more likley ...
written 22 days ago by i.sudbery2.7k
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Comment: C: How to convert transcript level TPM to gene level TPM ?
... transcript_tpm is the name of the dataframe, not a column in it. ...
written 23 days ago by i.sudbery2.7k
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Comment: C: How is it possible to have more than 25000 genes in counts file?
... and 58,000 is about right for the full gene set including non-coding. ...
written 29 days ago by i.sudbery2.7k
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Comment: C: should I merge fastq files for different lanes before do QC?
... Its a good point, but as far as I'm aware the only mapper that uses information from one read to inform the mapping of others is STAR in 2-pass mode. I'm pretty sure tophat doesn't. ...
written 4 weeks ago by i.sudbery2.7k
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Comment: C: Did you remove ChIP-seq duplicates
... Yes. Don't do short read single-end ChIP-seq. ...
written 4 weeks ago by i.sudbery2.7k
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Comment: C: Fold change - a final explanation
... Well, that depends on the program. None of the standard rnaseq programs report regularized logs as default I don't think, other than DESeq, and even then it outputs the non-shrunk values as well. ...
written 4 weeks ago by i.sudbery2.7k
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Answer: A: Fold change - a final explanation
... There is what appears to be an error in your definition of fold change (could be an error, could be causal wording): * A fold change describes the **ratio** of two values (not the difference). i.e. (expression condition 1)/(expression condition 2) * The log2 fold changes are the log-of-the-fold-c ...
written 4 weeks ago by i.sudbery2.7k
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Answer: A: Which Operating System Do You Prefer For Bioinformatics?
... Most stuff we do is done on a linux HPC that runs CentOS. People access this in different ways, but my preffered set up is a big windows box (Xeon, 32GB RAM) running a Xubuntu VM (which gets 20GB of that RAM). I have SSHFS pipes set up to the disk areas on the HPC that allows me edit code in local ...
written 4 weeks ago by i.sudbery2.7k

Latest awards to i.sudbery

Scholar 5 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Commentator 6 days ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Popular Question 4 weeks ago, created a question with more than 1,000 views. For List of replication dependent and independent histone genes
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 9 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 9 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 4 months ago, created a post with more than 5 votes. 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 5 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
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?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Popular Question 6 months ago, created a question with more than 1,000 views. For UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 6 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 6 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?

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